Modifying Paleo for Autoimmune Conditions (i.e., The Autoimmune Protocol)

May 10, 2012 in Categories: , , , by

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NOTE:  This is no longer the most up-to-date version of the autoimmune protocol.  You can see the most current version here.

Autoimmune conditions and a leaky gut go hand in hand.  In fact, in every autoimmune condition that has been tested, a leaky gut is present and is a contributing factor to the illness (not all autoimmune conditions have been tested, but many in the paleo community assume that leaky gut is a factor in all autoimmune conditions).  For individuals with suspected or diagnosed autoimmune disease, additional dietary guidelines exist to help address the disease.  In many cases, autoimmune conditions can be put into full remission by following these guidelines.  There is some variability to these guidelines depending on who you ask, so I have reviewed them and compiled a comprehensive list of not only dietary restrictions but also food recommendations using information from The Paleo Solution, The Paleo Answer, and various podcast and YouTube interviews with Robb Wolf, Prof. Mat Lalonde and Dr. Terry Wahls (author of Food As Medicine and Minding My Mitochondria).  These are all great sources for more information.

It is vitally important to adhere to a strict paleo diet with no cheating.  While other people may be able to enjoy the occasional bowl of rice, if you suffer from an autoimmune condition you are not one of these people.  Grains and legumes should never be consumed.  Dairy of any kind (even grass-fed ghee which can still have trace lactose and dairy proteins!)  should be avoided initially (most people will not be able to successfully reintroduce dairy, although some will be okay with grass-fed butter and ghee).  This may be true for the rest of your life.  In addition, if you have an autoimmune condition, you should completely avoid:

The reason is that each of these causes gut irritation and/or increased gut permeability (and in the super sensitive gut of those with autoimmune conditions, they just aren’t tolerated).  There is also some evidence that hormonal birth control can contribute to hunger and digestive hormone disregulation, leading to inflammation.  However, you may wish to address the other elements in this post before going off birth control, depending on your personal circumstances.

Dr. Terry Wahls lays out a very convincing argument for increased vegetable intake.  Her focus is on eating vegetables from four main groups:  green veggies (for the vitamin B, A, C and K content and the mineral content), colorful veggies (for the flavonoids and polyphenols; at least 3 colors per day but this includes brightly colored fruit like berries), sulfur-rich veggies (cruciferous veggies, veggies from the onion family, mushrooms and asparagus), and iodine-rich foods (seaweed).  Dr. Wahls recommends eating 3 cups per day of each of green veggies, colorful veggies and sulfur-rich veggies as well as at least once serving per week of seaweed.  Note:  If you have Grave’s Disease or Hashimotos Thyroiditis, you must also avoid goitrogenic foods, which include raw cruciferous veggies, radishes, spinach, peaches, and strawberries (cooking reduces the goitrogens; fermentation increases them).  I also recommend an extra serving of seaweed each week as well as at least three servings per week of oily cold-water fish to support thyroid function  (except in the case of Hashimotos Thyroiditis as there are mixed reports of iodine taken either as a supplement or in iodine-rich foods actually worsening the disease).

Meat quality is very important as this profoundly impacts the types of fat that you consume.  It is extremely important to be mindful of your omega-3 to omega-6 fatty acid intake ratio, aiming for between 1:1 and 1:3, as this is essential for regulating inflammation in your body.  The best way to do this is to ensure that all of your meat, poultry and fish comes from grass-fed, pastured or wild sources. Oily cold-water fish (like salmon, mackerel, sardines, herring, kipper, anchovies, trout, fresh tuna, and carp) should be consumed at least three times per week for their high omega-3 content, easily absorbed protein, vitamin D and selenium content. Grass-fed meat also contains Conjugated Linoleic Acid (CLA), known to reduce inflammation, promote healing and even fight cancer.  The nutrient profile of pastured/wild meat and fish is superior as well.   My post on the importance of grass-fed meat contains some suggestions for incorporating it into your diet in a budget-conscious way.  It is also extremely helpful to incorporate organ meat into your diet at least twice per week due to its high nutrition density (including some amino acids, vitamins and minerals that are not as concentrated in muscle meats).  Note that the high vitamin A content of liver may be contraindicated in anyone consuming foods that they are allergic or sensitive/intolerant to as it has potential adjuvant activity (it may be better to add liver into the diet after 3-4 weeks of following this protocol).   It is also more important to eat organic produce as much as possible.  Whole9Life has a wonderful chart on when fruits and vegetables are in season including which fruits and vegetables are important to buy organic and which aren’t, if budget is an important concern.

Autoimmune conditions are also typically associated with disruption of normal gut microflora, often including Small Intestinal Bacterial Overgrowth (SIBO).  For individuals with suspected or confirmed SIBO, avoidance of starches and sugars other than monosaccharides (like glucose and fructose) is very important (read my post Fruits and Starchy Vegetables with Small Intestinal Bacterial Overgrowth for a list of which starchy vegetables are okay and which to avoid), although this is one aspect of the autoimmune protocol which is highly individual.  Some people do extremely well with the inclusion of starchy vegetables in their diet. For those with gut dysbiosis (any condition in which the type, amount or location gut bacteria are not normal), it is also important to help repopulate the gut microflora by eating raw fermented foods (like sauerkraut, coconut milk kefir, or kombucha) or taking a dairy-free probiotic supplement. Some people may need to avoid high FODMAP fruits and vegetables (which I discuss in this post) as FODMAP sensitivities are common in those with leaky guts and/or gut dysbiosis (when the lining of the gut is damaged, there tends to be fewer fructose transporters so any sugar or starch containing alot of fructose is harder to digest).  Others will need to limit themselves to cooked vegetables, which are typically easier to digest.

Healing the gut becomes very important.  I highly recommend consuming bone broth, organ meat (note the caution against consuming liver initially described above), oily fish, and coconut oil on a fairly routine basis as well as making sure that you are getting adequate vitamin D, whether you are taking a supplement, food sources like liver and fish, or spending lots of time outside. Note that coconut oil does not contain the phytic acid or inulin fiber (both gut irritants) that other coconut products contains (a little coconut is typically tolerated, but I urge caution).  Stress management is very important and I highly recommend doing at least one of the following: go for daily walks, take up yoga or tai chi, take a class on meditation, or make time for an activity/hobby that you absolutely love.  And I cannot emphasize enough the importance of getting lots of good quality sleep.  Aim for 8-10 hours of sleep in a cool, pitch-black room, preferably waking up without the use of an alarm.  It may help both stress hormone regulation and improve sleep quality to drastically reduce your caffeine intake.  Aim for no caffeine if you can.  It is also very helpful to drink plenty of water and to make sure you are consuming enough food.  The body is not very efficient at healing itself when you are running a caloric deficit (you shouldn’t have to gain weight to heal, but losing weight may be a competing goal for now).

I know from experience that this is a very challenging task.  I also know from experience that 90% is not good enough (and the more serious your condition, the more important compliance is).  I know from experience that this increases your food budget (although perhaps this can be negated by decreasing your medical expenses).  I try and focus on the delicious foods that I do get to eat.  I try and focus on the fact that I have a strategy for improving my health that is far more powerful than any prescription medication (Note that in many cases you will still need to be on prescription medications although you may be able to reduce your dose.  Please work with your doctor on this one!).  And, compliance gets easier once you start to see improvement.  Are these restrictions for ever?  Some may be and others might be successfully reintroduced after you see improvement in your symptoms. What foods you can reintroduce when if highly individual and will be the topic of a future post.



I don’t have a diagnosed autoimmune condition but have been experiencing chronic pain in my lower body for several months. I’m about to embark on an autoimmune diet to see if it will help with my symptoms but am wondering about coconut products other than oil. Is coconut milk and butter ok? The safe choice is probably just to leave them out but including them would make the rest of the diet so much easier to stick to. Thoughts?

I am so glad I found your site! This is wonderful. I am trying to follow the multiple sclerosis 30-day plan in the Practical Paleo book but eggs are included in that plan whereas you are suggesting not eating eggs. I’m not sure what to do. Also, I hate fish. Is there a way I can get the benefits of eating fish without having to actually eat it? The one fish I eat is Sole and I never see it on the recommended list of fish to eat. I just can’t envision forcing myself to eat something I hate. And how can I be sure I am getting the right balance of Omega-6 and Omega-3 in my diet? Lastly, what about snacks between meals? It looks like fruit is a no-no while trying to heal the gut – do you have suggestions for mid-morning and mid-afternoon snacks that stave off hunger.

Sorry for all the questions! I’m excited and eager to do this!

I definitely recommend no eggs. All fish is a good source of omega-3s (with the exception of farmed tilapia and farmed catfish), so if you like sole, go for it. It’s just not as high as the ones you typically see listed. Other ways to make sure you’re getting enough omega-3 is to avoid nuts and seeds (which I would recommend for MS anyway), eating pastured and grass-fed meat, limiting chicken. And even though I don’t typically recommend fish oil supplements, that is another option. As for snacks, go ahead and try fruit. Better choices would be something like jerky and same veggies. You may also want to see if you can increase the size of your meals and not need snacks (which might just not work for you, but maybe worth a try).

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Double drat…I am so addicted to coffee. But I think I need to dial in a little bit further as I have many of the issues listed. I hear you on the 90% rule being insufficient…what about 99% say like one cuppa per day??
is tea allowed? Although I do love everything about coffee the smell, sight, ritual of the whole thing ultimately I drink it for effect ie: caffeine/keep going. I may be ok w/ a switch to black tea to get over the hump.
thanks so much this blog is pretty awesome, love your wonky science woman approach :)

How is one cup per day 99% (do you normally drink like 100 cups per day?!)? I would try and go a good month without any coffee and then see how you do when you have a cup. Yes, tea does not pose the same issues as coffee (although it can still mess with your cortisol). I still drink black tea. :)

I am wondering if you have a list of all vegetables and fruit, or just foods in general that are allowed with autoimmune conditions and the ones that aren’t. I am just starting paleo and it’s quite overwhelming to understand what I can and can’t eat. A comprehensive list all in one place would be so helpful :) And you may have one that I’m missing. I am wondering about juicing. I currently drink 1 to 2 Mean Green juices per day. They each consist of 1 head of kale, 2 green apples, 4 stalks celery, 1/4 lemon, and 1 english cucumber. I feel good after drinking them but I can’t buy any of this produce in organic (because I live in the middle of no where in po-dunk America and I’m lucky to even find kale at all..Ok stepping off of that soap box). Do you think I should stop juicing or cut back. I’m a little concerned after reading the list (you recommended) of veggies we should be buying organic and the ones we don’t have to if budget is an issue. Thank You so much for taking the time to share the way you do. You are impacting so many lives for the positive!!

Hi Natalie,

I haven’t put any food lists together for the blog yet, but I am working on them for the book. In the meantime, this e-book has some food lists and Anne Angelone is actually coming out with a new e-book in a couple of weeks that is essentially a very comprehensive food list with sorting out FODMAPs, starches etc. if you can wait that long.

As for the green juices, I think some juicing is okay, but they pack a pretty powerful sugar punch (when you remove the fiber from the veggies, the sugars in them are much more easily absorbed). I typically recommend limiting to a 4-6oz glass of vegetable juice with meals. As for organic versus inorganic, organic is clearly better, but if you can only stick to organic for produce on the dirty dozen list (which changes year to year, but leafy greens are typically included) then I think you’re doing well. And then for anything inorganic that you buy, if you can’t peel it (which will get rid of most of the pesticides), then soaking in salty water for 15 minutes and then rinsing well is typically fairly effective.

Thank You for the information! I ordered the ebook and am very happy with it. If you think to please post a link on here when Anne Angelones book is released and I will check it out as well. I am a little confused on the sugar content of the green juice. The green apples were all I thought was sugar. But I don’t really have any I seem to be allergic to everything and it’s random. I got so frustrated with it that I just drank green juice for 35 days. It was really nice to not have random (yes random, not because I did or did not eat) blood sugar crashes all day, to not crave food constantly, to not feel hungry all day, and to not be congested, oh AND to sleep! That was some amazing sleep. I was losing weight too which had been impossible for me. I actually lost so much weight (17lbs which I’ve gained back 10 for. no. reason.) that my skin was getting loose and I decided to start working out. Well that was the end of the juice fast. haha I could have eaten the doors off the cabinets I was so so hungry. Anyway I feel like I am back at square one and I’m really glad I found your site. I have often thought of just juice fasting again but I realize that is not a way of life that I can maintain long term. After thousands of dollars to 3 differents ND’s (who were all helpful at some level) $1200 on blood testing to find out what food I am intolerant too, avoidance diets, and the list goes on and on. I have essentially spent my 30’s fat and unhealthy. My eyelashes have nearly all fallen out and my hair is thinning. I just feel like I want to be well so badly but I don’t know what to do. We’ve spent so much money and I’m back at square one. Which is why I am really excited to do this plan. I somehow managed to carry a baby full term 2 years ago so I have a toddler I want to be able to care for energetically and not feeling like every single bit of energy I use is the very last I have.
Um this site is for venting and not just questions right?lol I’ll stop there. If there is any information that you could recommend on living with edometriosis I would be glad to read it. That is my autoimmune disease. My doctor said it’s everywhere. I had two softball size cysts removed just before I got pregnant and I want to have another baby but I can feel that the cysts are back. No more surgery for me though! I searched for endo on your site and I read one very helpful article. But any others you could recommend would be great! Thanks again!

I have a question about a few foods. One website for AIP diet said no fruits, another said in moderation, what is your best suggestion? Also one site listed green beans as OK, another said no, again what is your best suggestion? I’m just starting on this adventure after going gluten and dairy free, then took out night shades and corn. Now have decided to go AIP at the suggestion of a friend. I have something similar to your lichen planus. It also looks similar to dermatitis herpetiformis. Thank you for any information you can share.

I say fruits in moderation, 1/2-1 per meal. Regulating blood sugar seems to be especially important for the skin conditions, as is probiotics and getting enough fat soluble vitamins (basically making sure you’re eating fish, organ meat and high quality animal fats). I say no green beans (okay for standard paleo, but not for AIP) at least at first. They are a food you can play with adding back in once your symptoms are improving. Good luck!

Thanks for your help. I thought the gluten and dairy free was complicated!! Glad about the fruit because I do like it, especially the berries and peaches. I’m also hoping that this takes care of the itchy spots that I have. I take probiotics and will need to acquire a taste for organ meat….not my favorite at ALL! Do you suggest taking supplements of the fat soluble vitamins? Are there any baked goods allowed on AIP? Thanks again

I have been dealing with Hashi’s, muscle pain, joint pain, chronic diarrhea, fatigue for a few years (since having kids). Been clean-eating, all organic, doing yoga, and as chemical free as possible since having kiddos because they do so much better that way. Recently went gluten-free for me and found that all muscle pain, all joint pain, chronic diarrhea, and fatigue gone. My question: how do you know if gluten-free is enough? Is there a way to tell if your gut has healed? Do you go by symptoms alone? I’d say I’m 60% Paleo because I enjoy the recipes, but I am not auotimmune Paleo at this point (still use eggs, tomatoes). Reluctant to go autoimmune Paleo it if I don’t have to since I cook for the family and we are all very slim. I appreciate any help so much! Thanks for taking the time.

Hi Sarah,

Two questions regarding the AIP …

First, when you say “no eggs”, does that mean only hen’s eggs, or does that include all eggs, from any kind of fowl? For instance, are duck’s eggs also prohibited? My daughter tested positive for IgG/IgE sensitivity to eggs – but, from your post, it sounds like under the AIP the issue is not the food sensitivity as much as the lysozymes. Does this issue carry over to duck’s eggs as well?

Also – why are green beans prohibited on the AIP? They are definitely our go-to vegetable, and I thought that they were a non-starchy vegetable.

Your website is incredibly helpful – thank you!

I mean no eggs. But when it comes to reintroducing, you might want to try duck or goose eggs and stay away from chicken eggs completely (an IgE reaction is not likely to go away). If you are allergic to one, you might be allergic to the others but you might not. Green beans are a legume. Most people can handle legumes with edible pods, but i don’t recommend them on the AIP because people with autoimmune disease are much more sensitive to the saponins in them. They might be successfully reintroduced later though.

I’ve been reading your site for awhile and I sure appreciate all the valuable information you share and put out there for us readers. In my case, it’s my husband who has the digestive/stomach issues – heartburn, strong reactions to certain foods, especially dairy, etc. We’ve been mostly following the Paleo diet for about 8 months now. Both of us have seen great health benefits from it as far as energy, feeling good and for me, post-baby weight loss. My husband however is hitting another setback. After months of feeling great, his heartburn seems to have returned again. We are now thinking that maybe he has a sensitivity to foods we have been eating. He saw a gastro doctor and together they feel he has the SIBO (leaky gut). Therefore, we are going to try some of the modifications that you recommend here. However, in his case he is actually hoping/trying not to lose any more weight. He wants to gain weight. He is six feet tall and only weighs about 155 pounds. He has 0% body fat. Do you have any food suggestions on how he can heal his stomach without losing any more weight, perhaps even make recommendations on how he can safely gain weight? We’d sure appreciate any insight you have!

I have Hashimoto’s and have recently gone grain free and working on completely eliminating nightshades to which I discovered I am very allergic. (Thought I was in the clear with a chicken paprikash recipe and have learned about paprika the hard way.) Also cut out sugar and dairy, with the exception of butter. I was tested by an allergist and do not appear to have egg or nut allergies. For purposes of gut healing, it is essential that I eliminate eggs and nuts if I am not allergic? And why is it that I can’t eat spinach or sweet potato, they’ve become something of a staple? But as other posters here have indicated, it’s a one step at a time sort of thing so I shall inch my way along in pursuit of better health.

I am very grateful for the information you share and the time you are willing to take to share you knowledge. Thank you very much.


This website extremely helpful for someone with Hashimoto’s and Psoriasis. I have read so many books on nutrition and health and giving up gluten and dairy and plant-based lifestyles and it is all so overwhelming and confusing. I am looking forward to your book “The Paleo Approach” coming out in September. Wish I did not have to give up grains and legumes too, I feel like my diet is going to be so restricted already with no gluten, dairy, nightshades and goitrogens, there is not much left. Thanks for all of the wonderful information on your website, it is one of the most informative I have ever come across.

Can’t wait for your book to come out! To have all this amazing info compiled all in one place it’s going to be great…I Did the AIP last November/ december…didn’t see any changes…then Christmas came and although I’ve maintained a “paleo diet” it hasn’t been the AIP…New lesions of the condition I have continue to appear…Starting again, this time it will be easier because I already know what it takes, so there is not much suffering plus no major expectations, except feeling great :-) If my condition improves- all the better! if not, at least I know I’m getting healthier. The bone broth really does make a difference and the caffeine free lifestyle, although sad and lonely :-( (I love my coffee!), make a difference in cortisol stability, I definitely felt the difference when I didn’t drink coffee for six weeks. What is your take on juicing…I’ve been doing this daily since I started the AIP protocol and have continued…I usually include Kale, Romaine lettuce, celery, cucumber, carrots, dandelion roots and one apple– do you juice, is having the raw veggies a good thing? Also, do you own a vitamix? It seems to be all the hype with healthy eating, was wondering if you own one and what you use it for? Also, plan on getting the 21 day detox book…is this ok to while doing the AIP- it seems to be more or less the same idea- no sugar….veggies and protein only?

Hi Paleo Mom!

First of all thank you so much for your website! As a twenty-year-old kid, I feel like I am always the only one that is taking care of myself and eating healthy, only to constantly get comments from my family and friends that are not supportive. Your website has helped me a lot because you support everything so well with scientific evidence, I am very thankful for that.

I am currently restricting FODMAPS and following The Autoimmune Protocol. I have been very strict about it and it hasn’t been too hard for me, I am actually very excited about all the positive effects. I was already eating a high raw Paleo diet before I found your website, but I have found soooo much great new information here. I recently got a pretty bad reactive arthritis due to an infection (or so the doctors think, they are not sure) and they have prescribed me the NSAID Naproxen, though I was sad that it would be breaking my Autoimmune Protocol, I’m really hoping it will help my other health conditions which have been very bad recently.

So I have two questions: if I’m following the Autoimmune Protocol will taking the NSAIDs ruin it?
Also is there anything I can do to reverse some of the negative effects of the NSAIDs on my gut? (other than following the Autoimmune Protocol otherwise.) Possibly drinking lemon juice or raw apple cider vinegar with the NSAID?

Thank you so much for your website and your help!

Taking NSAIDS will perpetuate a leaky gut, but you may be able to wean off after being on the AIP for a while (important to work with your doctor on this one). But, you won’t be able to fully heal until you can go off of them. I don’t recommend doing any food reintroductions until you can go off NSAIDs and steroids.

Okay thank you for your quick reply! Also, because of FODMAPs and the Autoimmune Protocol, the vegetables I can eat has become very limited, so right now my vegetables consist of leafy greens, carrots, zucchini squash, green beans, and cucumber, but I read somewhere on this site that the seeds in some of those vegetables can cause GI problems. Is this true? Should I not eat them for right now?

Hi there,
Would this eating regime be considered too radical for complaints of asthma (could be considered as seasonal), hay fever and eczema (throughout the year and quite debilitating). I tried Gaps for 4 months, strictly on the intro diet for 1 month, and didn’t see any health changes other than a 15lb weight loss that I didn’t need! My known allergies are environmental; house dust mites, grasses, molds etc., not really any foods.
Would the theory be: that if I didn’t have a leaky gut, my immune system would be able to handle the environmental allergens?
Thank you so much for any advice you can offer!!

No, it would not be too radical, and if you didn’t have much luck on GAPS, it might be a really good place to start (I would normally recommend starting with standard paleo but no nightshades). I would suggest eating a good amount of quality animal fats and keeping the intake of lower starch starchy veggies like squashes up on the high side to try and keep the weight on. If you don’t see improvement in 1-2 months, I would look at liver detox supplements (typically selenium and molybdenum, talk to a functional medicine specialist for dose and brand), FODMAP sensitivities, and histamine sensitivity (see as possibilities. Good luck!

I was diagnosed with Grave’s disease after the birth of my youngest child, about 35 years ago. I was treated with radioactive iodine, and subsequently became hypothyroid. Thyroxine supplementation brings my thyroid hormones within normal range. Am I still considered to have Grave’s disease, and therefore need to avoid raw cruciferous fruits and vegetables?

I’m in the process of researching and revamping the raw cruciferous veggies recommendation for my book. The problem seems to be excessive quantities in a selenium-depleted diet, which doesn’t apply if you are eating fish or if you are eating a variety of veggies. So, at this point, no I don’t recommend avoiding them. But I also don’t recommend eating only cruciferous veggies. :)

Hi Dr. Ballantyne!

I’m currently following the AIP and FODMAPs. I have two questions.

I’m on prednisone due to a reactive arthritis. I saw in previous replies that you said this will interfere with the AIP, is this true and why?

Also, I have trouble not being hungry, especially because my vegetables are so restricted and I try not to eat more than 2-3 servings of fruit a day (is that necessary?). I’ve been eating at least two pounds of meat a day (either grass-fed beef or wild-caught fish), is that too much meat? Also, what can I eat to feel more full? I’m always hungry! Would plantains be okay? Anything else you recommend to feel fuller?

Thanks in advanced and thank you so much for your website. You really are improving the lives of so many people, including mine. I can not thank you enough for that.

Prednisone directly opens up the junctions between the cells that line your gut, causing a leaky gut. It’s not simple to just go off of it though and you need to make sure you are working with your doctor on that one. You’ll want to make sure you’ve got the AIP down pat before you taper and make sure you keep going with strict AIP for 1-2 months at least afterward.

Plantains are okay if you can handle the starch. That really depends on whether or not you have bacterial overgrowth and how regulated your blood sugars are. It’s worth trying.

Increasing the portion of vegetables you can eat and a good fat source will help with feeling more full. That might mean making a dressing with olive oil and lemon juice or apple cider vinegar for your veggies, or adding some coconut oil, or eating fattier cuts of grass-fed/pastured meat. Your appetite is also artificially increased from prednisone, so being able to taper off of that will help dramatically.

Hi Dr. Ballantyne!

I asked you previously about prednisone and a leaky gut, but my doctor told me that now I’m going to have to take either a DMARD (they said methotrexate) or a TNF inhibitor (such as etanercept, infliximab, or adalimumab). Will my leaky gut be able to heal while on either of those?

I asked the doctor, but they don’t even recognize that there is a connection between leaky gut and NSAIDs or steroids…

Thank you so much for your help. I feel like I should be paying you for your advice lol. I will definitely be buying your book!


One of my hopes with the book is that a patients will be able to bring it to the doctor and point to the information and all the referenced studies to be able to have a more informed and ultimately more helpful discussion. From a leaky gut standpoint, the TNF inhibitors are a better choice than methotrexate (which does cause a leaky gut). I hope this helps!

Okay thank you very much!! I’ve read somewhere that cannabis is a TNF inhibitor, and I used to smoke marijuana about 3 times a week but I quit since I got sick a month ago. In general do you think smoking weed is okay with the AIP / leaky gut? If you don’t know the answer I understand. Thank you so much for your help!

In general, I recommend no recreational drug use with autoimmune disease. I haven’t researched cannabis specifically, but I do know that it has been shown to potentially induce schitzophrenia which is a suspectd autoimmune disease.

Okay thank you so much for your help!

I just have one more question I’m sorry to ask so many, I’ve been unable to have a BM without Milk of Magnesia for the past four weeks or so. I’ve been on a strict AIP with absolutely no cheats for two and a half weeks (except for the NSAIDS I took for 3 days and the prednisone I’ve been on for 3 days), can I expect the constipation to go away soon? I’m worried I’m going to become dependent on the MoM. If I don’t take MoM I just don’t go… is this problem likely to persist until I can get off prednisone to heal my leaky gut?

Again, you’ve really been sooooo helpful in relieving a lot of my stress about my health. I can not thank you enough for the peace of mind, as it’s been a really difficult and depressing month. Thank you.

It should go away, but it’s hard to say how long since it depends on a bunch of factors. Was constipation a symptom you had prior to AIP? Are you eating enough veggies? Are you getting enough sleep? Are you drinking broth and eating organ meat?

I’m sorry I swear this is the last question! Over the past 5 days I have become completely addicted to the dehydrated kale chips I’ve been making.

Now that I think about it, it’s a bit suspicious how quickly I got addicted to them, I made sure to take the time every single night to prepare them for myself for the next day. I realized I was eating 1/2 – 1 lb. worth of raw, fresh kale every day.

I checked this on nutrition data and apparently that amount has more than 40 g of carbohydrates, which is what I’m now suspecting caused my addiction and voraciously quick eating of all of them every morning from my dehydrator.

I started wondering about the type of carbohydrate in kale. I suspect I have SIBO, and I pretty much stay under 100 g of carbohydrates every day, but if I think I have SIBO, is it better if most of those 100 g of carbs are monosaccharides, so I don’t feed that overgrowth. Or is (what I think is a complex carb) a complex carb like in kale better? (what kind of carbohydrates are even in kale?)

Sorry I started typing my question about the kale before I saw that you replied! Yes constipation is an issue I’ve been having for the past 6 months pretty badly, but always had to some degree for years. I eat a lot of vegetables and always make sure to get my sleep, but I’ll definitely get on the bone broth. (I’ve been eating sooo much organ meat, I always crave it.)

The reason why I ask about the bone broth, is it could be a melatonin deficiency (and the glycine in bone broth can help support neurotransmitters in general). Once of Chris Kresser’s recent podcasts had a discussion about supplements to support melatonin (the transcripts are all online so you can search for it fairly easily). You could try Natural Calm as an alternative magnesium supplement. I also recommend getting a squatty potty. As for the kale, you could be enjoying them because they are so nutrient dense (if you crave organ meat too). Carbs in kale are most likely short starch molecules. It does have a lot of insoluble fiber, which can be an issue for some people, but that’s usually more in the context of also eating a lot of sugar. I guess it’s a fairly easy experiment to try a week without them and see if it makes a difference…

Okay that would definitely make sense about the melatonin since I have been having sooo much trouble sleeping! I will definitely be making myself some bone broth and I will look for that podcast. I have made myself a makeshift squatty potty out of a box :) Thank you so much for your help!

Hi Dr. Ballantyne,

I know I’ve been asking a million questions, I’m sorry I’m just so worried! I’ve been suffering from a reactive arthritis for about a month now. Five weeks ago I ate raw beans (sooo dumb of me) and then had diarrhea for two days, then a week later the reactive arthritis started. I have not cheated at all while on the AIP for a little more than two and a half weeks now (except for the prednisone and naproxen…)

My reactive arthritis seems to just not be improving, even though I’m on prednisone, which was supposed to shut it all down. My problem is autoimmune in nature and I have a family history of serious autoimmune problems. It’s really conflicting for me trying to decide what to do, because I’m following the AIP strictly, but I feel like the steroids I’m on are ruining it. Do you think my problem would go away if I got off the steroids and didn’t take any NSAIDs and just followed the AIP?

Thanks so much again for all your help,

P.S. I’m a 20-year-old male and I listen to your podcast! My roommate walked in the other day when you were talking with Stacy about shampoo… awkward haha. Also I actually stopped using shampoo about a year ago, I only use soap to clean my hands! It’s the way to go!

At least we weren’t talking about feminine hygiene products! lol! I would advise patience. No, you won’t be able to heal completely while on prednisone and naproxen, but you need to wean/taper and I would advise doing this with the guidance of a health care professional. But, the good thing is that you should be able to heal some now and the healing will speed up when you can get off NSAIDs and steroids. How long is your course of prednisone and what dose are you at?

And please, call me Sarah. :)

Okay sorry, hi Sarah! And yeah good thing that would have been much more embarrassing haha!

I’m currently on 25 mg of prednisone a day and every three days my dose is going down 5 mg. I was hospitalized 10 days ago on Monday (I probably should have gone to the hospital about 3 weeks ago, but I was stubborn about it, my parents finally convinced me) and they made me stay in the hospital until Thursday. What I was just realizing is that I started getting better within 5 or so days of starting the AIP (about 4 days before I went to the hospital) and then worse since they started me on NSAIDs and prednisone! (since starting NSAIDs / prednisone the pain in my feet has gotten worse, but the overall swelling is down.)

Realizing this I’m so mad I went to the hospital and I’m so mad how little the doctors know! I was improving up until I went to the hospital, but since they’ve put me on NSAIDs and prednisone, the swelling has gone down but the pain has only gotten worse. It’s so ridiculous that they prescribe NSAIDs and prednisone for an autoimmune problem when they perpetuate autoimmune disease!

I’ve also become really passionate about Paleo and especially the AIP (because you!), but it is soooo frustrating trying to convince my friends and family because they don’t want to believe grains are bad, “the science isn’t there”, etc… I started thinking all the time “Damn, I wish I was really rich so I could fund tons of research to show people how important it is to eat this way!” I’m currently an economics / psychology major but I’m starting to realize that it would be so much more meaningful to me to actually do that research myself. I know you have a PHD in biomedical research, would that be the ideal degree to be a researcher on nutrition / autoimmune disease? Would that mean I should major in biology in my undergrad in order to do that?

The whole point of me writing this book is to help patients have more productive discussions with their doctors and validate this approach for discussions with family. So you have about 10 days left of prednisone? You really do need to taper, so I think you’re kinda stuck for now. Hang in there.

Really, you can get at medical research from any science degree. My undergrad is actually in physics, then I did a PhD in medical biophysics, and the last research I was doing was cell biology (I just became more and more biological as I went). Biology, biochemistry, physiology, microbiology would all be great places to start. And there’s so many different angles to the research that needs to be done, you could be in a graduate program in so many different areas (biology of which there are many subfields, or something more clinical like nutrition sciences). I would recommend taking a few entry level courses and seeing what’s the most enjoyable for you and the most natural for the way you think. :)

Okay thank you so much for all your help and for being so responsive! I’ll probably wind up having another question in the next week, so I’ll stop promising this will be my last post :) But really, thank you so much for answering me and for having such a great blog. I visit your website more than any other paleo/health blog because it is organized so nicely and so informative! I will also definitely be taking some intro science courses next semester and seeing what I like!

Has anyone posted a sample meal plan for the aip? Lots of comments so maybe I missed this somewhere. My head swirls every mealtime with all the things I “can’t” eat that I am lost on what I can! :) thx

Hello, I was told that fermenting goitrenic foods actually decreases the goitrens. What is your source for fermentation increasing goitrens? It would be great to know as I have Hashimoto’s and eat saurkraut nearly every day.

I’m actually in the process of completely revamping the goitrogen recommendations (I’m going to recommend not limiting them) but I’m still going through the scientific literature on this. I will update this post once I have that 100% figured out.

Thank you for your awesome information! I have done numerous tests through Cyrex and Genova and have a slight autoimmunity and several food intolerances. However, almonds, walnuts, and eggs were VL…Am I safe to eat these or should I stay away because of my Leaky Gut and Autoimmunity? Thanks so much.

You would probably heal faster without them, but if you wanted to try keeping them in you could. I would just point out that nuts quantities should be kept very low and egg whites can be a problem even if you aren’t sensitive.

Hi Sarah!

I don’t know if you remember me but I asked quite a few questions about a week and a half ago. I have reactive arthritis (or so the doctors think, they said there is no way to confirm this), so I have swelling and burning pain in my feet and left knee, my blood tests show very high inflammation markers, and I also have an HLA-B27 genetic marker that makes me more susceptible to reactive arthritis. The past month has really been miserable, I can’t walk at all, getting up to go to the bathroom with crutches is very painful, and I cannot do any of my school work. I finally got off of prednisone, I took my last dosage on friday. I haven’t seen any improvement since then (I know it can take a while to heal a leaky gut), I’m following the AIP 100%, drinking bone broth, taking probiotics, lots of coconut oil, eating organ meat, lots of wild caught salmon, and taking natural calm.

My family is so unsupportive of my diet. They constantly are negative and they won’t take the time to look into it online. I don’t know how to convince them. I’m starting to think they’re just all idiots. The doctors wanted to put me on a TNF inhibitor, but they is known to potentially cause terminal cancer. I think I’d rather try this first… I feel sooo pressured to get better, as everyone in my family thinks that my diet is causing my problem (even though I started the diet AFTER getting sick). My sister is also suffering from a very serious auto-immune condition, she can hardly breathe, and she is on huge doses of prednisone, which I am really worried about. I’m trying to convince her to just try this diet, but my dad gets very angry at me for telling her that. I’ve showed them your website and other things but they just refuse to believe it could have merit!

Where on the carbohydrate curve do you think I should be to heal my leaky gut? I’ve been under 100 g / day, is that too low? Is it also important that I keep my fruit to only 2-3 servings a day? Also, raspberries have seeds in them, should I not eat them because of that?

I also went to an acupuncturist yesterday. He said that there is too much dampness and heat in my body. He recommended that I take an herbal concoction. I’m open to trying it, but I’m worried it could perpetuate a leaky gut. The way it’s made is all the herbs are cooked in water and then I drink the liquid. The herbs that he recommended are :
-Cassia Twig
-Peony Root
-Liquorice Root
-Fresh Ginger
-White Atractylodes Rhizome
-Common Anemarrhena Rhizome
-Divaricate Saposhnikovia Root
-Prepared Common Monkshood Daughter Root
The whole herb combination can be seen here:

Do you know if drinking those will be okay in terms of the AIP?

Thank you so much for your help. I wish I could give you a hug or something I don’t know how I can ever repay you for your help. I can’t wait for your book to come out, especially so I can show my family. Thank you so much!

I think around 100g is probably good, but really anywhere between 50g and 200g if you are eating low glycemic index veggies (anything less than about 65). This should allow you to eat a tons of non-starchy veggies, and a few servings per day of lower starch starchy veggies and a little fruit.

As for the herbs, that’s really not my area of expertise (and I haven’t even heard of half of those ingredients). You might benefit from talking to Anne Angelone at and checking out here teleclasses for the autoimmune protocol (next one starts at the beginning of April).

Hi Sarah,

I apologise in advance for the length of this mail. I will try to be as concise as possible.

I have an autoimmune condition that is, for now, not definitively diagnosed (it could be one of a number of conditions). I have known this for years but I try not to pay too much attention to it and just get on with my life. I do not take any medication and manage things through diet and lifestyle choices. My doctors and neurologists support me in what I do (their advice is “keep doing what you’re doing”).

For almost 15 years I did not eat any red meat or chicken. I have been eating fish since about 2006. From a grain perspective, for about ten years, I ate only whole grains, spelt etc and avoided overly processed products. I ate very little dairy (usually goats’ products) and lots of fruit. Recently, I started eating liver and chicken and I think I feel a positive impact of that – especially the liver. I drink about three mugs of chicken bone broth a day (usually before each meal or included in soups).

I think I may have a huge number of food sensitivities/an exceptionally leaky gut. I say this because when I eat ANYTHING I get a build-up of mucus at the back of my nose and the base of my throat. When I wake up in the morning the mucus is there. Some mornings it is more severe than others and when I blow my nose there are often traces of blood on the tissue. The mucus stays pretty much the whole day but can increase, depending on what I eat. I have had this sensation for a long time but in recent years it has gotten much worse. I know for sure, that certain foods will increase the mucus e.g. sugar, dairy, pasta (the usual suspects). However, something as simple as dill can also increase the production (I have fresh, organic dill in my kitchen and while passing it yesterday, I tore off a little branch and ate it. Almost immediately, I could feel the impact).

I thought perhaps the issue might be FODMAP or SIBO so I have eliminated these foods from my diet. However, even foods that are permissible under AIP, FODMAP and SIBO still cause problems. Today, I discovered cinnamon is a no-no (my leg gets heavy and there is increased mucus production) and dates caused so much build up I had difficulty breathing!

I get bloated quite easily, however, since removing grains from my diet this has improved a lot (but not totally). I have seen an ENT specialist and I do not have sinusitis or any other infection. He tested me for allergies to wheat, milk and eggs and all came back clear (I do not eat these products but he still tested). He did say that I have very narrow nostrils but nothing that should cause problems. His advice was to have a procedure that would widen my nostrils and increase air flow. He could not guarantee this would make a difference to the mucus build up though. I don’t think it would help – it is not addressing the root cause of the issue.

In general, I eat very healthily and my plan is to continue with AIP, FODMAP, and SIBO. However, I have one weak area in my diet. Because of the mucus, I am conscious of bad breath so I chew gum when I know I am coming in contact with people – obviously, gum is full of artificial sweeteners and other nasties (things that would never, ordinarily, make their way into my diet) and it is not something I like doing, however, I do not want to repel people :)) and I have a business to run… In recent days I have started sniffing olbas oil in an attempt to clear my nasal passages. I regularly wash out my nostrils with a salt solution. I take peppermint tablets to relax my colon (sometimes, once I’ve taken these, I can taste peppermint, indicating, perhaps, a little reflux. This does not always happen however, so I don’t think I have constant reflux). In the past, I have tried bentonite clay and psyllium husk to try to cleanse my intestines – it didn’t work so well as the psyllium husk had a lot of difficulty completing its journey :) . I have been toying with the idea drinking a little bicarbonate of soda diluted in water before bed to see if it will make a difference (my father has done this all his life and swears by it for regulating digestion).

I am beginning to despair that I will never be normal! I am very outgoing but this problem is really taking its toll and making me very self conscious. I am also convinced that this issue is linked to my autoimmune situation. I think getting a handle on this would have a very positive impact on all aspects of my wellbeing.
I’m sorry for the long email; I wanted to give you as much information as possible. I’m hoping you can answer the following questions:

In addition to the AIP, FODMAP and SIBO plans, is there anything I can do to help heal the gut?

Do you have any, natural, replacement for gum that will serve the same purpose?

Can you estimate the length of time needed before an improvement is seen?

I know this is not going to be a quick fix however I would really appreciate any help you can give.
Thank you,

I’m sorry to hear about your health battles. It’s highly likely that the mucus production is linked with the autoimmune issues, but I’m afraid I have no insight into what exactly that might mean in terms of diagnosis.

As for diet changes, I suggest focusing on micronutrient density. Lots of organ meat, offal (things like trotters, cheek), fish, and vegetables (that will be mostly non-starchy vegetables for you with FODMAP and SIBO restrictions, but you should still be able to get a really good variety). Broth is great. Make sure you are getting enough fat and getting enough carbs through the higher starch low starch veggies like carrots, winter squash and pumpkins and maybe a little fruit. You might want to try digestive enzymes as a supplement and see if that helps. The baking soda doesn’t really sound like the best idea to me. But, if you don’t have a clotting disorder, ulcers, or are taking NSAIDs, you could try a stomach acid supplement (best info at A high quality probiotic may be useful (I like PrescriptAssist). And you might want to get some food sensitivity testing and avoid any highly reactive foods for a couple of months.

Also, I can’t stress enough the importance of sleep and stress management.

You should start to see some improvement within the first couple of months, but it could take even a couple of years to see full healing.

Also for the gum replacement, you could try a lemon juice and water or apple cider vinegar and water rinse or even maybe add a little food grade peppermint oil like a mouth wash and see if that helps. Liz Wolfe (from Cave Girl Eats, who I defer to for these sorts of things) recommends Basic Breath Spray from Tropical Traditions and Neem Chew Sticks from Neem Tree Farms.

I hope this helps!

Thank you Sarah for such a comprehensive response. I will let you know how I get on with the food alterations.

I do not live in the US but I will look for the products you suggest online. Do you have a preferred brand for the digestive enzyme?

Have a lovely (Saint Patrick’s) weekend.


I use the one from Tropical Traditions, but more out of convenience than because I’ve compared brands or anything. I have heard that NOW foods makes a good one.

Bien Venu!

Just wanted to let you know – I went looking for this page on the site and had a bit of a hard time finding it. I don’t see a link to it anywhere under the “Autoimmunity” menu – I finally found it under the “Eating Paleo – Paleo Modifications”. Seems like it should be at the top of the Autoimmunity page – maybe it is but I just couldn’t see it…

Thanks so much for all of the your education here – sooo looking forward to seeing in the book! :-)

I’ve been eagerly “devouring” the info on your blog last couple of days and have decided to do the AIP Protocol, since going dairy free/gluten free has not entirely gotten rid of my psoriasis (although it has vastly improved). Unfortunately, I cannot seem to incorporate leafy greens in the amounts suggested by the Paleo diet/ AIP protocol without suffering a severe gastrocolic response. I’ll spare most the details but it causes adominal spasms which rival the most severe menstrual cramps (I’ve seriously almost fainted at times) all in an attempt to evacuate my entire digestive system whether I want to or not. Maybe this issue will clear up once I’ve adopted the AIP for a while but for right now, I’ll just stick to small amounts of leafy veggies. If however, it doesn’t clear up, what would this type reaction seem to indicate? Can people have sensitives to excess fiber in their diet?

Hi Sarah,
Thanks for your wonderful website — chock full of good info. HOPING you can answer a question that no other paleo site seems to be able to answer. Here goes:

I’m hypothyroid, recently diagnosed with Hashimoto’s. I have been gluten-free, dairy-free, soy-free for years. I am now also strictly egg-free, grain-free, nightshade-free and mostly sugar free. Zero processed foods, and get worse with all chocolate and coffee, so I stopped them too.

Started with selenium supp a few months ago which INITALLY caused incredibly positive change ( lost 5 lbs easily), but its positive effects suddenly wore off, and I had a bad autoimmune flare up…including sudden severe swelling of the thyroid/throat – AFTER trying to implement the clean, veggie laden paleo protocol that sites such as this one advocate! I cannot tolerate even highest quality meats and poultry, animal fats. It makes no sense!

I had previously found some success with a 90% raw food vegan diet and juicing. Annoying way to live, though, and I lost even more muscle tone and memory function.

Any idea why someone would be totally unable to process meats and animal fats?? Same with coconut milk, meat and coconut shreds/flakes (though coconut oil is fine). No good. My body blows up immediately, I gain weight overnight, breasts swell as if I’m menstruating.

Digestive enzymes don’t help this situation.

I cannot find any references to such a dilemma on your website or any other. Do some folks have an inflammatory reaction or intolerance to dense proteins/fats?? I desperately want to heal with food, but am at my wit’s end, being seemingly unable to go paleo.

Thank you!

There are a variety of possible causes for the flare. I could even be completely unrelated to diet and be attributable to stress, spending less time outside, not getting enough sleep. It could have been caused by a viral infection or it could also be the development of a new food sensitivity.

I think getting your iodine levels checked is probably a good idea. Both too little and too much iodine can cause problems with Hashi’s. And one of the aspects of supplementing with selenium is it changes how your body processes iodine. How much selenium were/are you supplementing with? Too much selenium can also cause problems by itself (you may have overcorrected which is why it helped initially and then stopped helping).

It is also very common to have digestive problems when your thyroid hormones are out of whack. So, the inability to digest meats and animal fats may be directly attributable to the flare. Also autoimmune thyroid diseases have a tendency to occur at the same time as celiac disease or primary biliary cirrhosis, two additional autoimmune diseases that can affect digestion. Here’s a paper about it:

I would suggest adding other forms of digestive support supplements to digestive enzymes to see if that helps. Specifically, I would add an HCl supplement (check with your doctor since these are contraindicated in people with ulcers, taking NSAIDs or other blood thinners, and people with blood clotting disorders) and I would add an oxbile supplement. Also, the proteins in fish are typically easier to digest (fish is also a natural source of selenium and iodine).

I also can’t emphasize enough the importance of getting enough sleep and managing stress.

I hope this helps,

Thank you so much for your insightful, detailed reply.

5 months ago I began supplementing (and still am) with 200mcg of a high quality selenium supplement (one by Life Extension, another by Thorne) per day, along with Magnesium, which my body seems to need. Didn’t think of fact that I maybe overcorrected

My stress levels haven’t changed and are in fact fairly well managed, and I sleep well and adequately. I am gluten sensitive, though I do not have Celiac. I do already take HCl, but have never heard of oxbile. Will check that out.

Interesting re iodine — everyone says iodine is oil on a fire for Hashi’s, but I’ve been skeptical. It does always seem to irritate me each time I try to use it.
Do you have a particular test kit/lab that you prefer for testing deficiency? The patch test is obviously unreliable.

I have always had problems processing meats and fats, especially nuts (as well as coconut flakes, cream, meat), for as long as I can remember. My younger sister is the same way, so I suspected that just certain body types were unable to handle the paleo diet. Also, I know that in MS, also an autoimmune disease, there is much controversy over consuming animal proteins and fats, as it is said by some to worsen the condition. I wondered if the same mechanism was in play here.

Deeply appreciative,

Hello, Sarah. Such an informative site, and what a supportive voice for many seeking help! Hoping to start AI protocol for family member, but I need to have something to present to the family member that will convince that it will help Hidradenitis Suppurativa, especially since it is Stage 3, and has been going on for over 20 years. Thank you!!!

Hi, I am interested in the Paleo diet for Autoimmune disorder. I have been suffering with Hidradenitis Suppurativa (HS) for over 7 years now and am at my witts end with this disease. I have read about people controlling or totally eliminating this disease with the Paleo Diet, specifically for Autoimmune disease. I am having trouble putting it all together though, and feel a little overwhelmed about not being sure of what I can eat and what I cant eat. Is there any kind of list out there that is cut and dry and what you can and cant eat for this specific diet? I want to give it 110%, but I really need to be sure of what I can and cant eat before I start. If you could help or direct me to a list I would appreciate it!!

I think a good place to start in a standard paleo diet if that’s not what you’re doing already. Hidradenitis Suppurativa is a suspected autoimmune disease, but not confirmed. If you’re really gung ho and want to get started with the Autoimmune Protocol, I recently reviewed an e-book that is a great resource.

I would also direct you to Tara Grant of who cured her HS with a primal diet.
I hope this helps!

Hi, your site is lovely. I have been very ill and am interested in doing the autoimmune protocol…have hashis. Is there a list of foods somewhere that I can eat. I saw the avoid and the general categories but am wondering if there is a more detailed list and perhaps recipes for what i can eat…and also fruit?

Thank you,

I have RA and also an ongoing battle of digestive issues that flare up periodically. The last 2 weeks have been hell. Extreme pain and bloating and I feel like my insides are going to burst like there isn’t enough room under my ribs. I bought a bottle of digestive enzymes two days ago and it has helped TREMENDOUSLY! I can’t wait to implement these additional changes and see how much better I can feel. I can actually wear pants again today without pain. Hopefully this autoimmune paleo diet will help resolve the residual inflammation inside. I think my entire small and large colon have been extremely inflammed.

Thank you, PaleoMom, for such a helpful article.
I was wondering whether you could clarify your suggestion on twice-weekly servings of seaweed? What constitutes a single serving of seaweed? A tablespoon of dulse? A sheet of nori? I know different seaweeds are widely variable in their iodine content…. How much seaweed do you suggest consuming each week?
Thank you!
Kind regards,

WOW such a wealth of info again from PaleoMom!! Thank you!! :-) A few weeks ago, a gave up startchy vege to see what happened! I had already removed Deadly Nightshades few years ago (I have Psoriatic Arthritis)…Also I am started the Autoimmune protocol Paleo PROPERLY- this time! I went Paleo on 1st August 2012 because I was utterly sick of being a fatigued, floppy muscled, tubby-chubby vegan with a thyroid problem!! I was never chubby until I was vegan for a while, I never had a thyroid issue either….I had been GF for many years too… Over the years I was always lead to believe that being a vegan was the best thing for Psoriatic disease, and that meat “went toxic” in the human gut (false pro-vegan claims)….Anyhow, turning Paleo fixed my thyroid issue (never used the drugs I was offered) new blood tests show normal T4, T3 TSH! I also lost loads of weight and look like my fit self again!! yay!

Polyols indeed give me horrid gas, sorbitols, things ending in ‘ols’ , low carb choc bars etc!!! Sugar free sweets OMG nooooo!

I have been only having green calm veggies..
I have stopped eating nuts too and eggs. I will re-introduce egg white and see what happens in a month..But with nuts I definately see redness increase after eating them…

If I stay really strictly to the AIP system, I may see some great results!!? The arthritis and skin flared really badly a few months after going Paleo, but I had suddenly started eating eggs again, and I was doing whey protein for the weight loss too, and even tried cheese!! …Also baking with nut butters, nut flours…So, having stopped that, I hope to see how I improve ! The flare was so bad that I was put on Chemo to stop my joints deforming. Now it is all calming and healing (even though I am left with bone deformity) I hope I can retrain my immune system to be ok.

I had noticed that is I fast/starve and dont eat anything at all, my skin is so much better, but that is just not sensible or practical! lol
I have started taking high dose L-Glutamine for gut healing too!
Seems like the joy of baking desserts is out for me…But I do jolly good savoury dishes! I love coconut, seem to be getting on with it wonderful!
Been through so many different diets in my life so far too. Though at least I got my energy back, and slimness! It is also like having to retrain your thinking, as when being a Vegan, you are brainwashed into believing certain things which are a load of rubbish. Everything I eat, I bless it with gratitude and thanks. <3

Thank you for your website! I just wanted to clarify, if I wanted to follow the auto-immune protocol, can I eat berries/fruit, corn starch, sesame oil and wheat-free soy sauce (the tamari sauce I have has water, soy beans, salt and alcohol). Some berries/fruit look like they have seeds in them, such as pineapples, strawberries, raspberries, blackberries, etc… If I can’t eat berries, can I eat blueberries since they don’t look like they have seeds in them? Thanks so much again!

Thanks so much! Just another follow-up: what about carbonated water, vinegar, pickles and cooking with alcohol (i.e. fish)? Thanks again!

It’s a common sensitivity, and if you are thinking of nutritional yeast, you need to make sure it’s not grown in wheat, but other than that, it’s okay.

Hi Thanks for all the info. I am wondering what your thoughts are on yams/sweet potatoes and autoimmune disease. I am wondering how an autoimmune disease can be healed when on these foods since according to GAPS/SCD they are dissacharides and therefore will not allow a leaky gut to heal.


I believe the gut can heal while they are in your diet and in fact, going too low carb can put a big strain on your thyroid function. That being said, I myself don’t tolerate sweet potatoes very well, I believe because they are high FODMAP. In The Paleo Approach, the only fruits or vegetables that are omitted are nightshades and legumes.

Hi Sarah– I’ve been on the AI protocol for two weeks now. A couple of things have come up that I’m wondering about:
— Why is it that once on the protocol I react strongly to foods that I (seemingly) didn’t react to before (or at least not in the same way)? For example, I was eating dairy and nuts prior. Yesterday, I mindlessly ate a spoonful of the pesto that I was making for my kids (some parm. and almonds in it). Then it tasted so good that I had another bite! About an hour after I began to have gas pain and bloating that I still have this morning. I rarely had these digestive issues prior. The same thing happened last week with alcohol. I decided to try one drink— and was keeled over in pain the next morning. I gather that this is normal, I’m just wondering why.

Sleep is a huge issue for me and one of the main reasons I started the nutritional balancing program and hair mineral analysis for my adrenal burnout. I discovered that I have heavy metal toxicity which is slowly being released through the program. I’ve been doing it a year and have had some bad sleep times. BUT it was getting better before beginning the AIP. As soon as I started the AI, I started having horrible sleep again–felt like I was wired at night. Because I’m not sleeping, I feel worse since beginning AI. My allergies are better–but I’m not sure if that’s just because some of the pollens have calmed down, or if it’s my own body. I’ve seen your recommendations for sleep and have done them all (this has been a problem for 30 years)– I’m wondering if you might have an idea about how the diet could be affecting my sleep(?)

Thank you so much for your thoughts and information!

I have a much more thorough explanation in my book, but basically, when you eat foods that your body is sensitive to, it tries to protect itself (in a bunch of ways). Once you remove those foods from your diet, your body slowly stops trying to protect itself because it doesn’t need to anymore. That’s good because it means you are healing, but if you do eat those foods, you can expect a much more dramatic reaction, since your body isn’t prepared anymore. That’s actually the whole point of an elimination diet–it makes it much more obvious to isolate problem foods. The good thing is that as your body heals more and more, eventually you will have a higher tolerance for many of those foods again.

The biggest thing I wonder with how your diet is affecting your sleep is what your carb intake is. If you are too low carb, that could be causing the issues. Try increasing your intake of starchy vegetables, and make sure to have a big meal at supper time (ideally about 4 hours before you go to bed) and see if that helps. Eating lots of fish, taking a magnesium supplement and taking a vitamin C supplement will probably help as well (these are all to help regulate cortisol).

Hello Paleomom!

Thank you so much for creating this article! I’m just about to get right into the AIP but have a few questions that I can’t figure out though.

How do I know whether a certain food is problematic for me? Since eating a very strict paleo/low fodmap diet, my IBS symptoms have disappeared, but I still flavour my food with cayenne pepper/paprika and eat roughly 6 eggs and a lot of macadamia nuts a day (I’m bodybuilding so I need roughly 2800kcal a day!!).

Basically, should I just cut out all the foods you’ve listed, or is it possible I can tolerate some of the foods. If it makes a difference – I’m 19, very athletic, and have mild asthma, acne, a leaky gut and I suspect SIBO. I don’t know how severe my condition is, so I’m not too sure how strictly I need to follow the AIP.

The next question is, I’m worried about the amount of supplements I’m taking, this list includes.

Slippery Elm Bark powder – 3 tsp 4 times a day
L-Glutamine – 3 tsp 3 times day
Betaine HCL tablet – one before every meal (usually 4)
digestive enzymes – one before every meal (usually 4)
Oregano Oil – 6 drops, twice a day (taking this for candida cleanse)
A gut health tablet, contains Lactoferrin, licorice root and glutamine – 3 times a day
vitamin b5 to reduce sebum production – 500mg tablet 3 times a day
A clear skin mixture, contains zinc, burdock and echinacea – twice a day
FIsh oil capsules – 3 with every meal (except breakfast when I have a can of salmon)
Biokult probiotic – 2 capsules, twice a day
cup of homemade bone broth with every meal, this counts as a supplement right? :)

Most of these are for leaky gut and I haven’t had any side effects from taking these, but it seems unnatural taking all these pills, and I’m worried so many supplements may be detrimental to my gut problem, rather than fix it.

Sorry for the all of text, and thanks for your help!

So, the first thing I will say is that if this is working for you, you should stick with it. But, I’m guessing you wouldn’t be asking me if it was working for you.

Because you don’t have an autoimmune disease, but do have some immune issues, I think you could use the AIP more like an elimination diet to figure out what you’re still eating that you are sensitive to (you mention that you eat nightshades, eggs and nuts and any one of those or all of them could be holding your healing back). I would suggest eliminating all of those foods for 3-4 weeks then adding back in one at a time. This will help you determine which foods you can handle (and it’s possible that there are many). But, there are some other culprits to think of here too. Intense exercise causes a leaky gut all by itself. Lack of sufficient sleep and unmanaged stress might be a problem. Are you eating enough carbohydrates for your level of training? Do you drink alcohol (which can hinder digestion and cause a leaky gut too)?

You are taking a lot of supplements and I think you could prune this back. Most of the supplements you are taking are designed for short term use. Some of the supplements that you are taking are immune stimulators (slippery elm, licorice root, and echinacea… Not sure about burdock). You are taking a whopping dose of glutamine. Clinical trials use .3-.5g/kg ideal body weight (there are also trials that just give a fixed dose, 30g per day is common). These studies have all been done in critically ill patients. I don’t know how much you weigh, but you are probably taking about 50% more than the top of that range. That’s a lot of oregano oil too… You might be stopping good bacteria from growing. Depending on the quality of fish oil you are buying, the fats can be damaged and could be causing oxidative stress. Fish oil has been shown to be very effective for short term use but potentially problematic for long term use for probably this reason. It’s much better to get your omega-3s from food (fish is the best source, grass-fed meat is good too). If you aren’t eating a ton of chicken, high omega-6 nuts (macadamias are okay) or really fatty conventional meat, a can of salmon a day is probably enough to balance your omega-3 to omega-6 intake.

I think digestive support supplements and probiotics are great. Other than that, I think it’s best to look to food for everything your body needs. Organ meat, fish, tons of veggies, glycine-rich foods (like anything off the bone, bone broth, organ meat) will all make a big difference. Sleep, not working out too intensely and giving your body enough of a break between workouts, and managing stress are super important too.

Thanks for your prompt response!

I’ve decided to do a strict 100% low fodmap AIP, at least for the next 6 months till I start uni. My sister and mother both have celiac disease, so I assume I’m a likely candidate for immune problems aswell, and there’s no harm in trying the full AIP.

The answer may change entirely on the person, but do you know how big of a contributor strenuous exercise is to leaky gut? I do heavy lifting 5 days a week for 45-60 mins, and I really don’t want to give it up, I’ve toned it down a bit in the meantime as I’m doing a Candida cleanse and have cut out the majority of carbs, I plan to reintroduce bananas/sweet potato (don’t think this is a nightshade?) shortly.

I’ve cut out the slippery elm bark powder for now, I think it may be a fodmap? (it’s causing gas/bloating). And thank you for picking up my L-glutamine dosage! I’m suppose to be taking 3 teaspoons split over the whole day, not 3 teaspoons, 3 times a day :) I’ve also looked into Dr Chris Kresser’s research regarding fish oil supplements, and I’ve decided to trade all my O3 capsules for a single cod liver oil capsule with dinner.

Finally there are a few foods that I’m not too sure a bout. In your updated page of the AIP, shellfish are noted as okay, however these are a common allergy/irritant, and many sites claim they contain harmful toxins. (I eat frozen mussels and squid)

Also I have a Healthy Gut complex supplement that contains Dry licorice root and Lactoferrin(a milk protein from colostrum). Many sources claim these are both beneficial, but the licorice isn’t in it’s DGL form and I am allergic to casein/whey, so I’m a little unsure about them.

One final question, will The Paleo Approach be available on kindle?

Thank you again again and sorry for bothering you so much!

Most of the research showing that intense exercise causes a leaky gut is either high intensity short rest interval training (like HIIT classes or cross fit) or cardio (cycling, running). If you’re lifting with good rest periods between sets and laying off the cardio and metcon, you should be fine.

Sweet potatoes are not a nightshade, but they are a FODMAP. Some other low FODMAP starches are plantains, parsnips, taro root, and lotus root. The two diet factors that have been shown in the scientific literature to have the most profound effects on gut bacteria are fiber (basically avoiding refined carbohydrates) and omega-3s. But I do find that low starch diets for a couple of weeks can be very helpful (but then you need the starchy vegetables to help good bacteria grow).

Shellfish are extremely nutrient-dense and I think the benefits far outweigh the risks (as long as they aren’t being grown in extremely polluted waters, but most of what we get in North America should be fine). Of course, if you’re allergic, don’t eat them.

I would definitely try stopping the healthy gut complex for now.

Yes, The Paleo Approach will be available on kindle.

Hi Paleo Mom,

I’m literally at my wit’s end trying to figure out what all my health issues are. It all started when I was 14 and I started having seizures. They progressively got worse until I had the damaged part of my brain removed when I was 21. Ever since then, I’ve had gut and skin issues. In 2010 I went gluten free and noticed a big improvement in my overall health. I’ve now been Paleo for a year and a half. I’m struggling with eczema, weight gain, swollen stomach, and fatigue. I’ve cut out eggs, nightshades, and now nuts. I was tested for Celiac Disease but it was negative, maybe because I was already GF for a few months. Please offer any advice you may have. I’ve gained 10 lbs in the last 4 months.

Well, the first thing that occurs to me is to ask how your sleep is? and stress management? have you had your thyroid levels checked? are you eating enough carbohydrates and eating nutrient-dense foods? are you eating enough (you body might be gaining weight due to the stress of eating too little, especially if you have micronutrient deficiencies)? have you considered digestive support supplements? Yes, the celiac test could have been a false negative, but there are plenty of ways that you can be sensitive to gluten that are not celiac disease and even that can not be tested for.

I sleep at least 8 hours a night usually. My stress has been higher than normal lately. My intake has not been lacking. I would have a 3 egg omelet with spinach & mushrooms, 1/2 an avocado, and kraut for breakfast, leftovers for lunch which could be chicken, venison, or fish with veggies, or a spinach salad with chicken or shrimp. I would have a banana or green apple with almond butter for a snack or a LARA bar if I were on the go. I used to take a digestive enzyme but didn’t see a difference. I had all my levels check a few months ago, and everything can back normal. I’m just out of ideas here.

I love this article and the comments and am finding it very helpful and informative as I consider the idea that this might be me, and that implementing this plan might be beneficial. I have also been reading Paul Jaminet, and am curious on your thoughts on his approach (reduce protein consumption, eat safe starches and limited fruit with a limit on carb calories of 400, eat fermented veggies, bone broth, intermittent fasting, and get majority of calories through fat). It sounds above as though your experience indicates safe starches may not e well tolerated (white rice, potatoes of all varieties). Would ths be accurate?

There’s a lot that I agree with with Paul (like not being afraid of starches) and quite a lot that I disagree with, especially for those with autoimmune disease. I am quite opposed to intermittent fasting and ketogenic diets for those with autoimmune disease (and the research supports me on this–I will actually be posting a teaser excerpt from my book that discusses this in the next few weeks). There is also no evidence in the scientific literature that limiting protein or carbs is even remotely beneficial for those with autoimmune disease. In fact, I don’t like the idea of people with autoimmune disease thinking about macronutrients at all, but rather suggest a focus on micronutrient-dense foods. When you think about not eating carbs, people tend to undereat veggies, and your body needs protein to heal. You need fat too and especially fat soluble vitamins, so I’m not saying limit fat, I’m just saying nutritional ketosis is not appropriate for people with autoimmune disease (with perhaps the exception of short term nutritional ketosis for those with neurological diseases). I do not recommend rice for people with autoimmune disease, but I think starchy vegetables are fine (have a look at the updated version of this post linked above). I think fruit is fine too, as long as people keep their fructose intake in the 10-20g/day range.

Hello Paleo Mom,
Thanks for all very helpful information that you give us. I cannot stop reading your website and all comments. I am also so excited about the book and waiting the delivery in 4-5 months.

My question is….do you support the consumption of Almond milk in case of autoimmune disease?

Hi Sarah,

great website, thanks a lot for these helpful insights. I’m looking forward to your book!

I’ve recently been diagnosed with rheumatoid arthritis. My rheumatologist put me on Prednisolon and Metex. I haven’t started the Metex injections yet because I’m afraid of the side effects (Prednisolon is just as bad, but I need it to get the inflammation under control). Right now I’m looking for a holistic or integrated approach to put the RA in remission. Sadly, neither my physician nor the rheumatologist are inclined to look for “natural” ways to reduce the inflammation.

I’ve known & incorporated some aspects of the paleo diet before RA was diagnosed, and I’m now trying hard to follow the autoimmune protocol. But I do find it hard to eat a lot of meat – I’ve never been much of a meat-eater, I prefer chicken, fish, eggs and dairy products. I’ve cut dairy products and eggs from my diet, now I’m afraid that I don’t get enough animal-protein and -fat. And my rheumatologist told me to avoid meat, especially red meat, as it’s supposed to promote inflammation, so now I’m a bit lost at what to do.

What would you suggest?

Kind regards

The recommendations in the AIP are extremely thoroughly researched (there are 1200 scientific citations in my book, which is written just as much to educate doctors as it is to educate patients). Finding it hard to digest meat is typically a sign of low stomach acid, so have a look at the digestive support supplements I mention in this post. You can do this by eating predominantly fish (if you also include shellfish, this is actually a very healthy way to implement the AIP), and some chicken (it takes several meals of fish per meal of chicken to balance your omega-3 to 6 ratio).

Hi Sarah, of all the sites that I’ve found re: the autoimmune diet, thepaleomom has definitely been the most helpful for me. The winning combo is the science, practics and your availability to answer questions. Thank you so much!

My question concerns accessing protein. Until 4 weeks ago I was an ovo-vegetarian who had no idea that all my whole grains and legumes were potentially worsening my auto-immune symptoms. Since I started the auto-immune diet however, I have had allergic reactions to at least chicken and lamb and I felt really sick in my stomach after eating beef. I tried eating more nuts to get more protein but that resulted in cramps and when I added eggs back into my diet after eliminating them for 21 days, I also experienced cramping. I’m hoping fish is the answer :) but I’m wondering if you have any comments about this? I ask this question because of a statement you made above about the fish in protein being more digestible than meat which you said may be relevant for those with severely damaged guts.

I should maybe also mention that until I started the auto-immune diet I relied upon legumes to stabilise my blood sugar levels which are wreaking havoc at the moment. Is there ever a time when you recommend eating legumes using the traditional/tried and true forms of cooking/preparing?

Thanks again. I look forward to hearing from you!

I definitely think fish is a good choice. I would also suggest looking into digestive enzymes to help support digestion (if you look at the updated version of this linked at the top, you’ll find descriptions of which ones I recommend). I guess if you were soaking, sprouting, fermenting and then thoroughly cooking legumes and introducing them after you’re feeling better, then I guess they’re okay. I would suggest some strachy vegetables to help with the blood sugar regulation and lots and lots and lots of sleep.

For the Autoimmune Protocol, can I eat something with carob bean gum or pectin in it? Can I chew gum with gum arabic in it? Thanks as always for all your help!

Also, can you tell me if I can eat something with sunflower oil in it (for the Autoimmune Protocol)? Thank you again!

Generally not recommended due to the high omega-6 content, but if it was only a little and occasional, it should be fine (for example, I might have a handful of dried cranberries as a treat and those are sprayed with sunflower oil).

Great site and very informative. I have had Hashi’s for 13 years and only till this year a Naturopath explained about Leaky Gut to me and the importance of diet. My biggest complaint is Fibromyalgia and food intolerance, primarily to the good foods. I’ve been on a elimination diet for 4 months but to no relief from pain. I have not eliminated all the foods on the NO list due to ignorance I guess, because not reacting to certain foods on allergy testing also. But I have not felt any improvements on my health.
I am just now starting to look into Paleo diet and realize I am eating many NO NO foods. I have been a vegetarian for 35 years and just have had to start eating fish and eggs due to too much muscle loss with my diet. What next? I don’t want to eat any other meats. Is there hope for me? How do you know your gut is healing?

I think you can heal very effectively if your only protein is seafood (if you’re just eating fish, I suggest trying some shellfish too because they are so mineral dense)–I care more that you are getting some animal protein, not weather it’s meat versus fish. You should slowly see improvements in your symptoms, increased energy, less pain, better sleep. Give it a few months before you start tweaking. If you were a vegetarian for so long, digestive support supplements are a very good idea (click on the link at the top of this post for the updated autoimmune protocol).

Thank you for your response. So for the last four months I’ve been on a gluten free and most cross reactives, soy free, sugar free, dairy free, fruit free diet and probably some other free foods too.
I am willing to be off more foods like nuts, seeds and nightshades, but if I don’t feel any better from my pain, I don’t know what else to do. I am taking supplements prescribed by my Doctor in Nutrition, they are all geared to healing the gut, but I thought as long as I am still eating tomatoes and some peppers and nuts/seeds that maybe thats whats holding me back from healing.
I can’t wait for the new cook book coming out soon. I looked in Barns and Noble but didn’t find any related to the immune system.
What are your thoughts on Brewer’s Yeast for flavoring and nutrition?

If you aren’t sensitive to yeast, I think it’s fine, but I feel a little hesitant to recommend it while you’re still dealing with pain. High omega-3 intake can be very helpful with pain. It that doesn’t help, you could look into low dose naltrexone.

Hello Mrs. Ballantyne! I have recently decided to change my diet in order to (hopefully) improve my life instead of depending fully on pharmaceuticals and doctors advice. I have been diagnosed with UC (colon removed a few years back), Ankylosing spondylitis and RA. I’ve looked into Paleo before but had never heard of nightshades or autoimmune protocol until I stumbled upon the terms tonight and googled them together to find your blog. I must say your posts are very informative. Considering I’m new to these ideas, are there any posts of yours that I should read first to get me going? There seems to be a whole lot of information on your site! I feel the need to thank you already for your blog, it seems to be exactly what I needed to find. Thank you!

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