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 have Hashimoto’s Thyroiditis which is now in remission thanks to the AIP diet. I still ate eggs and seeds and I am ok with that. I am now about 8 weeks pregnant and vegetable and meat make me so sick I can’t even look at them. The only thing that settles ok is brown rice.. Do you think eating brown rice again will upset my gut? I don’t want to trigger an immune response, but at the same time chicken and veggies trigger my gag reflex right now and I don’t know what to do. Any thoughts? Advice?

Well, often pregnancy hormones will suppress parts of the immune system responsible for autoimmune diseases and many people with autoimmune disease will experience a reprieve during pregnancy (this often goes with a flare after the baby is born or when the baby weans). So, I think that if rice is working for you right now, then that’s okay (white rice would be better than brown rice from an antinutrient standpoint). The protein aversions that are so common with pregnancy usually go away in the second trimester, at which point you can start focusing on nutrient density to hopefully mitigate a flare after the baby is born.

That makes so much sense. I had my first really bad dyshidrotic eczema flare up after my first son was born. It took awhile to figure out what it was and I actually self-diagnosed because all the doctors I saw had their heads up you-know-where. Thanks for all this great info. My Dad just started eating AIP per my instruction (for his psoriasis) and I really want to get your book! I’ve learned so much just from your blog posts.

I’m confused about some seeds. Chia seeds and flax seeds, are they ok to consume for autoimmune diseases? Do they have harmful lectins? I’ve heard such good things about these.

I don’t recommend chia or flax for autoimmune disease. Flax is crazy high in phytoestrogens. Chia is mucogenic, and while there are not studies showing that it is an immune stimulator, other mucogenic plants like aloe, slippery elm, and licorice root are all immune stimulators. Plus, the omega-3 fatty acids in these plants are almost completely unusable by the body.

Chia seeds make me bloat. Not good for autoimmune…although I do not think I react to flax. Good to know about them being unusable to the body.

i used to eat flax seed by the gobs, as in 32 oz plastic cups filled with ground flax and water each day for weeks at a time and i noticed beneficial effects in my back (discs?) and also where the ribs attach to the sternum. I was much younger though so my absorption and conversion from ALA to longer chain omega 3’s was likely much better but now i hear that saponin content in flax may be a problem so its prob not advisable anyway. To say that the body cant use the omega 3’s in flax is incorrect though imo.

Where would you suggest starting if I have hoshimoto’s autoimmune and salicylate sensitivity to quite an extreme. I notice you offered a list of high salicylate fruits, but what about vegetables? There is so much conflicting information on how to get beyond the leaky gut / salicylate sensitivity… but conflicting “lists” of food.

I would suggest starting with the autoimmune protocol, avoiding salicylates in household products and medications, and avoiding those foods that you know you have a salicylate reaction to. Salicylate sensitivity should go away as your gut heals and it’s quite controversial in the scientific literature whether there is any benefit to avoiding salicylates in foods since medications and household products are by far the biggest sources.

Dear Sarah.
Thank you for this informative post! I’m looking forward to your book and have pre-ordered a copy. In the meanwhile, I’m trying to decide if I need the full AIP or could start with something like strict Paleo and see how things go. As far as I know, I don’t have a commonly recognized Autoimmune disorder. I do have severe environmental allergies (all developed in the last ten years), chronic sinusitis, mild food allergies and a major problem with oxalate toxicity which is most likely the result of a leaky gut and endogenous oxalate production brought on by oxidative stress and nutrient deficiencies (most likely not diet related, but my body’s inability to use the nutrients that are available). I am working with an oxalate scientist to address the endogenous oxalate production, but I’m hoping to address the rest of my issues through diet, especially the leaky gut. Does any part of this jump out at you and make you think “Start the AIP now.” Or do you think going very strict Paleo to start with the intention of adding parts of the AIP or the entire protocol if necessary might work? I am currently following a Paleo-inspired whole foods diet, with very limited grains, beans, industrial oils etc, which is how I feed my young children. It’s helped, but obviously isn’t enough.
Thanks for your time.I appreciate it.

I think it’s worth trying a very strict Paleo diet first before jumping to the AIP. I also think focusing on more really nutrient dense foods (rather than cutting things like eggs and nuts out) makes a lot of sense (so more organ meat, more seafood, tons of veggies). I’d give strict paleo 2-3 months and then see how far you’ve come before tackling the AIP.

I’m so interested in this and think it would be very beneficial for me to give this a go. Having said that, I’m a vegetarian paleo girl (too many lab pracs with cadavers!) and use nuts and seeds to make up for my lack of meat. Do you have any tips regarding the cutting out of the nuts and seeds?

I am working on healing my leadky gut and was wondering if one also has candida albicans should one heal the gut first or try to get the candida under control first or address both issues at once. Any comments are appreciated. Thanks

Both at once. The diet factors with the most powerful corrective influence on gut microoranisms is high long-chain omega-3 intake (from seafood) and high insoluble fiber intake (from vegetables). Adding in broth or other glycine rich foods and nutrient-dense foods (like seafood, organ meat, and vegetables) will help heal the gut.

Thanks ThePaleoMom. Are there any options for getting omega 3’s from non-seafood? I was recommended Cat’s Claw as a great option for healing leaky gut. Have you heard anything about this herb? Thank you.

Not long-chain omega-3s which are the kind your body needs. If you eat exclusively grass-fed and pasture-raised meat, not very much poultry and no nuts or seeds, you can get enough without seafood. All plant sources of omega-3s are ALA, but you need DHA and EPA.

Hi PaleoMom,

Yes, all the meat I eat is grass-fed without hormones and antibiotics. I do also eat a lot of chicken, turkey and some pork but it’s all-natural with no hormones and antibiotics. Should I cut down on the poultry/pork and eat more meat and add some offals? Thanks.

Hi Sarah,
I love the work you are doing and sharing.

Have ordered and anxiously awaiting both books and bought others you have recommended in the past months. Great reading.

I was following AIP to begin with, as I have life long dairy, coconut and wheat allergies. Recently I had a kidney stone pass (agony) and the urologist is doing further testing at the moment. However, the diet she recommended conflicts with what I have been doing. For example-NO meat broths, game meat, dark green leafy veggies, turnip, cabbage, fermented veggies, limited protein, organ meat, but DO eat dairy. It is the typical diet recommended for kidney stones.

On top of that, I do have gallstones and a fatty liver which adds another layer of confusion for me. At the moment, I do not know what to eat, where to begin to get healthy again and I do believe the problems are all linked.

I would be interested to hear if anyone with similar problems has successfully followed the AIP? Many thanks!

Hi PaleoMom,

I cannot tell you how grateful I am for your site. I have literally spent hundreds of hours searching the internet to help me with understanding my son’s health problems. He has been chronically ill since he was 7 years old and is now 20, never having been able to attend school, hold down a job or play sports. We have finally found a wonderful microbiologist who is now on his case but the picture is overwhelming. Your site has helped me understand so much of her report, and understanding goes a long way to helping implement major changes.

A general summary of his problems would be Histamine Intolerance, Leaky Gut, IBS, Chronic Fatigue, and Anxiety. There are several other side issues such as his liver struggling, chronic infection, etc but this was the best summary I could give from a 30+ page report!

I have read a great deal of your site already but have alot to go, and have found answers to a great deal of questions. There are two foods which we have to eliminate that have me baffled – pineapple and almonds. Can you explain why these should be eliminated from a diet? (Other nuts are apparently ok, just not almonds or cashews). I was of the understanding that pineapple can be quite soothing for IBS so until now it has been a regular part of our diet.

Strangely enough, wheat is not on the list to avoid, however from everything I have read I still plan on eliminating it. Avoiding almond flour does make it a little tricky but coconut flour is fine, so we will focus on that instead.

Any light you can shed on this would be greatly appreciated.

Thankyou again for such a wonderful resource and all the time you put into it!

Almonds are very high in polyunsaturated fatty acids and cyanogenic glycosides. The PUFA are inflammatory, and the cyanogenic glycosides cause the release of cyanide in the body which can be a stress as well, especially if your son’s liver is struggling. Pineapple can stimulate histamine production, so that might be why (it’s also full of digestive enzymes, which is why it can be so helpful). Also, sunflower seed flour can substitute for almond flour in most recipes 1:1, so that’s a good option to consider.

I have not been diagnosed with an Autoimmune Disorder, but have been following Paleo for 3 weeks now. My main symptom I am trying to get rid of is Brain fog and Fatigue. Do you think this diet will help in those areas? Thank you!

FANTASTIC article. Thank you so much for sharing this information in such a succinct way.

I just have one question – I was diagnosed with celiac and I am wondering if the precautions mentioned above are for something like that or for more severe autoimmune conditions. I mean, I gave up gluten rather easily (except for living in a foreign country at the time and dealing with that fun miscommunication) and now I am moving forward into Palo (skipping eggs as well).

But for a person like me, how critical is it that I NEVER have coffee, nut butter, or a glass of wine. I’m not interested in cutting corners – trust me, I did a mini-cheer when I read about how paying a little more for food means paying less for medication in the long run. Big fan of taking care of my body. I just want to make sure I don’t over-do it as it does indeed affect those around me to a great extent.

I’d love your feedback. Thank you in advance.

I think it’s for all autoimmune disease, but what you do is try it for a month, then reintroduce those foods and see if you have a reaction. Chances are good that if your stress is well managed, you’re getting enough sleep and activity, and your diet is nutrient-dense, that you’ll be able to add those foods back in and enjoy them without negative health consequences.

Awesome, thanks so much. Like I said, I am willing to do what it takes, but I just like to have all the information. Your blog and entire website is fantastic. I am so grateful for the high quality information you are putting out there.

Has anyone been successful at healing their underactive thyroid, completely eliminating it by following the Paleo Diet? And I get mixed lists of foods that you can & cannot eat, items in question bananas, mangos, tomatoes & bell peppers.

I do plan to follow this AutoImmune Protocol to kick start the process as I am just now linking my gluten intolerance to my underactive thyroid & am amazed at the amount of info out there.

And what about fiber drinks? I drink a fiber drink daily to help control my cravings through the day. Should I avoid those or keep drinking them?

Thank you for all of your information!!!

The AIP is discussed in detail in Sarah’s book The Paleo Approach. You can learn more abut the book here: You may also want to join our new The Paleo Approach Community group on Facebook, there are lots of great discussions on various AIP/Paleo topics. The group has over 4,000 members, you can request to join here: — Tamar, Sarah’s assistant

I am so disheartened by all of this. I have Celiacs and Hashimotos. I have been diligent about no gluten and no grains. I lost weight being sick and now I have gained 4 pounds back but my thyroid blood tests are still coming back terrible. If I cut out nuts eggs and goat cheese what is left to eat? I was eating lots of protein–servings at breakfast lunch and dinner but now my doctor said to cut back because of my cholesterol. I have a wedding in July that I can’t attend because of food issues. I feel like life is over not to mention the depression that follows cause no one understands. There are so many Paleo People out there. Does any one really know what diet actually fixes the thyroid numbers is everyone just guessing?? When I limit my carbs too much I go to bed hungry and stressed out. When does the suffering end? Has anyone seen remission with diet alone?

Yes. I encourage you to check out who saw dramatic improvement with celiacs with this protocol. And check out and Also, if you’re on Facebook, there’s a group called The Paleo Approach Community with over 4000 members all using this protocol for their autoimmune conditions. You aren’t alone.

You should check out Chris Kresser’s website, and his new book Your Personal Paleo Code. I think I read somewhere that he talks about too little carbs and hypothyroidism and that some women just need more carbs (I am one) to feel better (white rice seems to help me). Eliminating gluten put my antibody numbers in the normal range, but I did not feel much better until I got my medication figured out (taken me over 2 years and am still working on it).

Check out for some great information on thyroid related questions.

Are you aware of the “vegalicious” site, by ELena Wilkins. She cured her hypothyroidism naturally. Check it out and good luck.

Hi Sarah, I have just completed genetic testing and it turns out that I do not tolerate sulfur and I have been instructed to remove it as much as possible from my diet. I’ve read Dr. Wahls work and much of the literature of AI friend paleo eating strategies but most of these empshasize sulfur rich foods. Is there a way around this? Thanks, Ryan.

I’m confused, with auto-immune (Hashimoto and possibly IBS), if you can’t use almond flour or coconut flour, do you avoid baking altogether or what do you use? Thank you for your help!

Sarah discusses flours used in Paleo baking (including some that are nut-free) here: Sarah has a section of recipes that are Auto Immune Protocol (AIP) friendly, you can view them here: The Paleo Approach Cookbook will contain over 100 AIP recipes. You can read more about the cookbook here: — Tamar, Sarah’s assistant

I have Hashi/celiac and I’m confused on how much animal protein (ounces) is safe to consume on a daily basis? Right now I am eating protein at every meal excluding dairy and nuts due to AIP protocol. How much is too much? I’ve heard too much animal protein will deplete calcium from your body..true?

Also I’m not consuming nuts right now but when I do I was going to bake with them but a friend of mine said baking nuts alters the fat somehow and it becomes toxic. How true is that? Thanks for all you do.

No, too much animal protein can not deplete calcium from your body (that has been debunked). Eating animal protein at every meal is perfectly safe. Just make sure you’re eating veggies too.

No, cooking nut fats does not make them toxic. Cooking oils beyond smoke point does oxidize the fats which is not great. But, if you’re cooing with nut flours, the fats are very stable and not oxidized easily. Plus the internal temperature of baking is well below smoking point.

Now I have the sufficient information to do something about my autoimmunity. Thank you so much. This will help me change my quality of life for the better. I am very grateful. Your blog is the best!

I know you have addressed the use of antibiotics (if they are absolutely necessary) and how to minimize gut damage, but I have been unable to find any resources addressing what to do when NSAIDs are prescribed or necessary – for severe acute injuries, surgery or unavoidable medical/dental procedures. For those with an autoimmune disease, is it ok to take them for a short-term period of time for recovery? Are there any alternatives? Is there anything that will minimize the negative side effects and gut damage (i.e. healing foods, supplements, etc.)? Should I follow your suggestions for minimizing damage from necessary antibiotics (like you did with the burn from the bacon)?

Hi Sarah

I have decided to go for the AIP diet, I have hashimoto’s disease and a spot of arthritis in my hip – even though I am only in my early forties. It already seems clear that I am in need of the AIP. I am nervous and wonder whether I should start with Paleo and then go for AIP or just jump right in ! Any thoughts or suggestions would be gratefully received.

Thank you and best wishes
Susan in Istanbul – we don’t have access to almost anything organic or organically grown/raised unless you spend huge amounts on private farmers, which I cannot do :(

Reply to Sarah in Istanbul: Sarah, I also have Hashimoto’s and pain in my left hip socket and IBS. I feel like I have been to college with all I have learned online. My daughter also has Hashimoto. After taking the slow approach (gluten/dairy/soy free), in hindsight, I wish we would have just gotten on AIP RIGHT AWAY!! At first, we didn’t even know it existed, but after having a blood/food sensitivity test, the eggs, nuts, etc. showed up there anyway. GO FOR THE GOLD, the AIP diet right away! My daughter and I also have severe yeast issues and have gone on Christa Orecchio’s Yeast Diet. Take the free, at-home test and just spit a dime-sized piece of saliva in a glass of water each morning for 7 days in a row. It has to be before you eat or drink anything! Check it 3 times within 45 minutes. If it floats, you are fine. If it grows legs, you need to go on yeast diet. If it sinks, there are more of them than you!, LOL, but has some truth to it! I paid a fortune for a 1 day stool test that showed not enough yeast to do anything about, when I knew I had severe issues. My daily spit samples have sunk like a rock!! I soak all produce in white vinegar for 20 minutes to help remove pesticides, mold, dirt, etc. Also, check out Christa’s site at The Whole, she has a list of the “Dirty Dozen” Veggies and the “Clean 14” which don’t absorb as many chemicals. I am thrilled that this “Yeast Diet” will take care of the yeast, take care of leaky gut and give my thyroid, liver and adrenal glands a big boost towards healing!

I have just been diagnosed with Graves’ disease. (I also have very well controlled type 1 diabetes for 25 years). The Graves’ disease was diagnosed by a blood test since I do not exhibit any symptoms. Currently not on any medication for this disease and would like to keep it that way.

Starting the AIP, however my doctor also says to avoid foods with iodine. Now being hyperthyroid, that makes sense since iodine is what is needed to make TH. Unfortunately that means avoiding seafood, which I love. Also increasing goitrogenic foods since they inhibit the making of TH. Not sure my body knows how to find a balance of TH.

After a month of this way of eating, how do I know that it is making a difference aside from a blood test? Therefore, does this mean I can never eat food with iodine? How do I reintroduce food groups if I have no symptoms now? I cannot take a blood test every couple of weeks that a food is introduced.
Just looking for some sort of plan on how to approach things.

These topics (how to begin, food reintroduction) are all discussed in detail in The Paleo Approach. You can read more about what is included in the book here: Other posts that may interest you include: How do I know the AIP is working? and Reintroducing Foods after the AIP: — Tamar, Sarah’s assistant


Hi Melissa, I’m in Melbourne too, I have Hashimotos and would be grateful to have someone else nearby to share local resources with

Help Paleo mom! I have just found out that i am pregnant, i have been following the AIP for 50 days and have started with introductions, but should i stop that? the thought of eating this restrictive untill…well untill when? the baby is due? I have ME and have had great sucess with the diet. Would any adverse reactions to food be harmful to the baby? I have a leaky gut ( much better now thanks to you) and have been following AIP and fodmap. so greatfull for answers !

Many people find that they do not have serious food reactions during pregnancy and can eat plenty of non-AIP foods for the baby. You will definitely want to discuss any dietary changes with your doctor. – Christina, Sarah’s assistant

i have hashimoto’s. so can i eat fresh water fish like carp to maintain omega 3 ratio. is carp low enough in iodine for consuming on a daily basis?

I have a question regarding limiting nuts. I know they can be hard to digest, but I always soak my nuts and re-hydrate them to make them more digestible. Also, in the GAPS diet it does not say to avoid nuts. In the first month or so yes, but after, no. Are you saying to avoid nuts forever? I do notice that sometimes egg whites effect me and other times not….which might mean it is not even them and it is something else.

Soaking does make them more digestible but does not eliminate the problem completely. The autoimmune protocol can be, but is not intended to be, a permanent diet change. It is an elimination/reintroduction protocol to determine and heal from your unique sensitivities. You may find that you can add nuts back in. – Christina, Sarah’s assistant

HI Sarah
I live in the Uk and many of our foods are very different to America however I have followed your auto Immune Paleo faithfully for 49 days and have lost 1 stone in weight so I am very grateful to you. I have Takayasu a rare auto immune disease and for the last days following the diet I have felt better, however I have just had a hair analysis done which is showing allergys to Nickel in particular the others I have already eliminated.
However on Saturday having been so successful, I thought I would try and introduce 2 small tomatoes, wrong move I have been so ill the tummy pains, temperature spikes and muscles spasms in my legs have just set me back so badly, so I have decided to stay on Auto immune diet as I seem to cope well with that.

My question is while I am awaiting delivery of your book not arriving until May 2014 are there any supplements or tests that you could recommend that may help me further. My last PET scan was clear but my consultant wants to put me on to Ritiximab and I feel the cause and cure is most definately in my food so I would like to avoid any more drugs if possible I have just completed 9 rounds of cyclophosomide and heavy doses of Prednisilone, now down to 4 mg per day.

Takayasu has such little research therefore if I can prove that the auto immune Paleo diet has such a major contribution to holding the disease at bay then I am willing to do anything as I know from your own health issues you have done the same and it may well help many more people with this disease.

I just know there is more to my food but don’t know where to turn for advice on testing or help, so I do hope you can help me in any way.

My food is now totally organic.

Many thanks for listening and hopeful of some further guidance until I receive your book.


If the AIP in and of itself isn’t yielding the results you’d like, you may be sensitive to one of the AIP-approved foods. Some of the most common ones are coconut, FODMAPs (possibly due to SIBO, something your doctor can test for), and shellfish. It can also be that you’re simply not eating enough or a wide enough variety of certain foods like veggies, seafood, and offal. Sarah’s book goes into more depth on troubleshooting. In the meantime, this post addresses some of those topics: – Christina, Sarah’s assistant

Hi Jacqui, Have had a host of seemingly unconnected autoimmune responses for most of my life (am 55) and only recently discovered a supplement for gastrointestinal support containing L-glutamine and others and cannot recommend highly enough for repairing the gut and feeling super! Have not felt this good for decades. Didn’t know I felt so bad. Read Dr. Amy Myers in usa website. Bought my supp in a health food store, chemist had a commercial less potent version which I started on then found something stronger. It is a powder called “Intestamine” but each country will most likely have a different version. Teaspoon in small amt of water once or twice daily. There was a shellfish version which I did not buy in case I had a reaction. ps I live in Australia. Cheers. Mxo

Hi Margaret,
Thank you for posting the information on Intestamine. Can you please tell me what other ingredients other than L-Glutamine are in the product. Thanks again.


Hi Margaret, many thanks for your advice I will certainly try anything to help me. I have Takayasu although too old (61) but young at heart by medical standards but all of my aorta is inflamed, I have had 9 rounds of cyclophosomide and heavy steroids but when ever I reduce below 6mg daily the aorta flares again. I know it is from my gut but here in the uk leaky gut is not considered they only dampen down the immune system which is not good.
so Thank You most sincerely for the information I will track down tomorrow.

Kind regards

I realize this comment section is from last year, however, I just discovered it!
I have an autoimmune condition called Primary Biliary Cirrhosis PBC.
I was diagnosed 2 years ago at the age of 46. 4 years prior to that I had put on 100+ lbs. I’m sure the many starches I ate to gain that weight contributed to my condition. The only way I’ve ever been successful at losing and maintaining weight has been to eat low carb. I followed Atkins. I’ve been eating Keto/Paleo for a few months now, unaware of the AIP. I have lost over 40 lbs but seem to be stuck now. I never had a problem with my blood sugar but now when I test it, even in the morning, it’s always between 105-125. My blood ketones are between .05-1. I’m not sure what’s going on. I feel great. My liver counts are fantastic and I’ve even reversed fatty and enlarged liver!
I need to lose weight tho. I’m stuck at 202 lbs. I’m 5”3′ and would like to be at a healthy weight. HELP!! Thank you.


Thank you Christina. I’ll check it out. I found a wholistic physician close to my home. I’ll be going there as well. They believe in paleo nutrition!! Big win!

Thank you Isabelle. I listen to his podcasts as well as Robb Wolf. I’m doing what they suggest. I actually found a wellness Doctor close to my home is practices exactly what jimmy and Robb talk about! I went today.

Hi Sarah and Christina! Thank you for all the effort you put in creating all these blog posts and answering the questions!
I hope you will have time to answer my question. I have a child, almost three years old. Just a few months after her birth we realised she has several food allergies. Later blood tests showed she has these allergies: gluten, cow milk, soy, eggs, walnuts, hazelnuts, peanuts. Unfortunately, those were the only allergens she was tested on. Later we realised that she does not tolerate any milk products, tomato, peppers (paprika), origano, celery, cranberries.
From your blog posts I believe she has leaky gut and that’s why she has all those intolerances, including gluten cross reactions.
Finally, my question is: can you help me help her? Where to start as she is a child? How to look for negative symptoms – I am not sure I can always tell if something is not doing good to her body.
Best Regards!

In moderation. Because juice can spike blood sugar and doesn’t activate the important digestion signals in your body that chewing food does, Sarah recommends having juices as part of a complete meal, not a meal replacement. – Christina, Sarah’s assistant

I have Hashimoto, and currently only partially diagnosed autoimmune arthritis. Along with the endocrinologist telling me I am carbohydrate intolerant, Syndrome X/hyperinsulinemia/pre diabetes (whichever you prefer) And factor in the degenerative spinal disease.
I am a painful mess to sum it up.
This morning I have discovered this idea of autoimmune diets, whilst being very unsuccessful using ketogenic dieting. I am however a very picky eater, and combining that with this, that even eliminates things I’ve been using on keto, I am not sure what exactly I can eat. I love spicy food, :/ and I have been using almond meal, coconut flour, meat, eggs, cheese, and heavy cream as major components of my intake. That plus coffee, spinach, coconut oil, grass fed butter, mayo, Z SWEET, Stevia, chia, flax, psyllium husk powder, coconut palm sugar, pumpkin seeds, zero carb protein podwer (Gnc isopure), Brazil nuts, almonds, cashews, and occasionally pistachios. Plus light use of tomato sauces.
Can I keep any of these items?

It’s ideal to eliminate all non-AIP foods for the best results. You can ease into it by giving up/replacing one food at a time if you need to. The more non-AIP foods you hang on to, the longer it can take to see results. – Christina, Sarah’s assistant

You’ve got to get Sarah’s book! And read the website page(s) above! I also have Hashimoto and had a bad case of IBS and skin rash/issues. #1 I got off of all gluten/dairy/soy and it helped a lot, but my stomach/IBS was still way out of control until I got off of #2 Nightshades (tomato, potato, peppers, eggplant). Yes, I know, that includes most Mexican/Italian; but, it is worth it to be healed! I also did a serious Candida Cleanse for 8 weeks which at the same time healed my Leaky Gut. Now, YEAH, the IBS is completely gone and my Leaky Gut is healed. I have had a light tomato sauce on a gluten free pizza with only a barely noticable response from my stomach. I may only do that once a month or so. Everyone is different! My daughter also has Hashimoto and handles some nightshades with no big deal. All nuts and seeds really effected me too. I have also added back in goat cheese and am fine with that. After the blood test to confirm the auto-immune, the “food sensitivity” test was invaluable so that I could temporarily eliminate those items and begin healing my “leaky gut”. Sadly, you cannot really heal until your gut is healed. What also has been INVALUABLE and Sarah promotes them too have been Dr. Tom O’Bryan and Sean Croxton and Sara Olson’s Health and Thyroid Summits!! Google them too, but Sarah’s book is foundational!!

Can you point me to the right direction in helping my 4yr old? Everything is geared towards adults. She has rashes all over her body, itchy inflamed skin that is hot to the touch. She screams and cries for help all day and night. We have been looking at gaps, scd and now aip. Just wondering if a low histamine diet would be a next approach? Maybe gaps intro would be right? There is so much info I dont know which foods to cook, eat raw? We have been to the dr and that would just be a life time of antihistamines and steroid creams! No thanks. Any thoughts would be helpful at this point. Thanks.

Sarah recommends starting with the AIP and then only making additional restrictions (like histamines) if the AIP is not yielding the results you would like. Whether you eat your foods raw or cooked is a matter of personal preference (Sarah recommends mixing it up). You can find Sarah’s posts on Paleo for kids here: – Christina, Sarah’s assistant

Hi, I suffer from alopecia areata. I was wondering if you have read or know of anyone who has had improvement with this auto immune disease by following AIP? My alopecia has gotten out of control since giving birth 6month ago.

I believe it contains nightshades. Sarah recommends whole, solid foods on the AIP as much as possible, not juices or smoothies, as chewing is important for digestive health. – Christina, Sarah’s assistant

Hi, Just wondering if the autoimmune protocol diet would be useful for treating vitiligo. I feel well, the vitiligo started in 2012 and is very widespread over my body and is itchy at times. I have slightly raised tsh and high thyroid peroxidase antibodies (but not off the scale). I have become gluten free but perhaps with cross contamination as I cook for the family.
Your advice would be most helpful.

I’m so confused…Is there an in detail breakdown of what to and what not to eat on AIP diet for Hashimotos and Hypothyroidism? I sure could use it…

I don’t like any kind of seafood, which is a huge bummer because I know how healthy everyone says it is for omegas, selenium, etc.
I seem to have a hard time with eating more than 1/4 cup of coconut per day and can’t have any nuts with AIP , correct? Almonds tend to make me bloated and I overdo nuts when they are in front of me.
I’m a chocoholic!! I’m trying to cut it out completely..
I read that those who crave chocolate are low on magnesium. So, I’ve been eating bananas and avocados but can’t overdo those because of high glycemic index for bananas and too much avo makes my stomach turn…
Ugh..I can only eat so many veggies before I’m just plain craving rice.
I feel like I’m missing something…I want some kind of nut butter but can’t have sunflower butter.

Any advise would be amazing…Or even if it’s directing me to your book or an article on your blog.

Warmest thanks and SO much appreciation for your blog! I love it!! I don’t feel so alone. :)

PS. Have you ever heard of Kim John Payne? He’s a family and child psychologist. I use a lot of his balancing techniques in my home and it’s helped bring my child on board with my diet. We cook together and our new diet lives with us with warmth and joy. You should check him out if you have not already. Perhaps it will help your family too. :)

I’ve just bought your book (is on the way now) but could you tell me if inside are some API recipes? I have Hashimoto and I thought that normal Paleo is enough to heal.
thank you

I’ve been searching for a solution to my problem, I have endometriosis, would following the AIP be of help to treating my condition? I have endo but it is the rare type, bleeding spots all over my small and large intestine. Every time I’ve got my periods these spots bleed in my tummy and the blood stays there.I have been having the most painful periods for all my life. This has caused intestine lesions and if things get worse surgeons consider a removal. My issue was discovered by false diagnosis taking me for a surgery to remove my appendix (these were the symptoms and the tests results said so too – due to blood free floating in my tummy- it was dangerous). During the surgery my surgeon saw the spots and had to do another cut to open my belly from above the belly button till under it. After running tests, endo was the answer. All doctors I consulted suggested artificial menopause to make endo less severe. I went through it for 9 months (after 3 months periods came). In the meantime a homeopath told me that I do not metabolise wheat so I stopped consuming it and felt great for 2 months, no intestine pain, no constipation. Things got worse and after reading about paleo I cut out any kind of flour, potatoes and rice. After months pain came back accompaning my periods and intestine pain and problems too. I reduced sugar and coffee intake and I smoked a lot less. Only temporary results again because now my period is not regular in flow or date so I am on the pill to ballance it for three months and my doctor suggested after this I should try to get pregnant, if tha tis possible since my tummy is full of adhesions. I would realy appreciate it if you could give me some guidance. Even doctors have given up on me and are desperate because they can not find a solution which is not that radical. Please forgive any mistakes, English is not my native language.

Expecting your answer with hope

The AIP can certainly help reduce complications from endometriosis, though it’s not a cure. Angie at suffers from it as well. – Christina, Sarah’s assistant

I have Sjogren’s Syndrome, Celiac Disease, Intracranial Hypertension aka Pseudo tumor Cerebri & elevated Tryptase level. I am also allergic to seaweed in addition to almost everything that grows outside! My tongue is geographic & inflamed from my diet. I am already gluten free. How do you suggest I follow your Paleo Diet? My allergist told me NOT to eat any fresh fruits or vegetables because of my elevated Tryptase level. I am really confused…I am just getting sicker & sicker!!! I really need to help but no one has any answers…

Are cooked or otherwise prepared fruits or vegetables okay? Sarah does recommend following Paleo or, even better, the autoimmune protocol as closely as possible for the best results for autoimmune patients, but sometimes additional restrictions need to be made for other conditions. Sarah has professionals available at to help troubleshoot the diet change. – Christina, Sarah’s assistant

Just read your reply…I didn’t know where to find it! I am only supposed to have very limited amounts of cooked produce. I am really confused by all of this because from my research on the Internet even meat can have high histamine in it! My Tryptase level is bordering on Mastocysis & if it gets any higher I will have to have a bone marrow biopsy. So is this consulting a free service or I am I charged a fee? I am tapped out financial from all my medical bills!!! I was hoping for a a straight answer but thanks…even doctors are no help! Rita

Hi! Thankyou so very much for all of your information! You are so very generous with your wealth of information. My husband and myself have recently (3 weeks) transitioned to paleo. I have also purchased your book, and am wading my way through!

Have you come across people who, when transitioning, experience significant food aversions? My husband has autoimmune disorders (lupus and hashimotos). He has started to have trouble eating certain foods (that have previously been enjoyed). Sometimes it’s the smell that puts him off, other times it’s the texture, and he can’t stomach them. The aversions have been simple foods such as coconut milk, fruits, salads etc. I don’t have autoimmune issues, and I’ve transitioned quickly and well. Are his difficulties because of the autoimmune disorders and it’s just going to take longer to heal his gut?

I thought I’d ask, I couldn’t find anything specific like this in your book.

Thanks again – Nicole

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