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.



What about sprouts from seeds, like for example, sunflower sprouts? And also, what about sauerkraut? A no-no for Hashimotos? Thanks!

Is sauerkraut a no no for Hasimoto? Also is almond or cashew butter not good as well considering not allowed to have nuts

Thank you for this information! I’ve been following the regular paleo diet for years now, without improvement and my doctors have never mentioned that I need to do things differently if I had autoimmune problems. One more question for you- I am breastfeeding my 3 month old. Would you recommend starting this protocol now, or wait until I’m done? I’m wondering if I will have enough to eat to keep my milk supply up. What is your opinion on that? Thanks!

To Aflores:

My dermatitis seemed to be linked to ulcerative colitis and Doctor’s aren’t sure what diagnosis to give my thyroid. I started with SCD with some improvement, moved to Paleo, more improvement, on to Paleo AIP. I was still having some problems with my skin peeling/crusting (of course happens to be on my face) and being bright red when flared. I eliminated nightshades, moved to fodmap. Once onions and garlic were gone, my flares have slowed way down and the burning, itching, set on fire feeling I have had for years is finally gone.

Along with the skin problem slowing, I no longer have diarrhea-my Ulcerative Colitis seems much improved with no rectal bleeding. I am due to have a colonoscopy soon on schedule, will find out then what I look like on the inside. I have added back a slice or two of tomato once a week and a small potato once a month. I tried corn-no luck. I have basically given up on grains totally. I seem to have found a formula which works for me.
BTW-I do not feel deprived. Feeling better is wonderful, much more wonderful than donuts or pie. Takes awhile to find alternatives, sites such as this one helps soooo much.
I am off thyroid meds and my anemia seems to be gone also. I am 58 now and no meds at all, which amazes the staff when I go in for checkups. I broke my leg a few years back, the Orthopedic Dr. was amazed I showed no arthritis-my reasoning to boot nightshades back to the wild. Nicotine is the most difficult nightshade for me to give up and I am working on. My weight is trending down (a very good thing) and my smoking is much less.

The formula which works for me-Paleo AIP, low fodmap, no nightshades (I cheat occasionally with about a tomato slice or two weekly and a once a month potato), NO ALLIUMS!

Hello. I looking for suggestions for next steps. I have done low fodmop and paleo ai for almost a year. I have made little to no progress. My testings all show normal thyroid and adrenals..though my tg..thyrogobulin was up ten times the norm. Negative for sibo and gastroparesis… I show low pancreatic and fatty acid profile from stool testing with gastritis and ulcers in my small intestine. I am not sure if I should eat any starchy veggies…they taste good and are less fiberous but I still am not shedding a pound. I have gained 18+ in a year wo food changing. Greens and sulfur veggies irritate me tremendously. I am at my wits end….just want to feel fluid again and not in joint pain fatigued and have black puffy under eyes 24-7. I did recently test positive for two MTHFR s….which i am learning about .. My point is..if I have been eating super clean for over five years shouldn’t I be better and able to lose weight and 24/7 bloat?

When you had your thyroid panel completed, did you include Reverse T3? My panels were all within “acceptable” ranges with the exception of RT3, which was extremely high. I was put on a slow release compounded T3 immediately. In addition, have you checked your cortisol and vitamin D levels? If your adrenals are wacked…you are putting extra stress on your thyroid. Balance is key. Best of luck! BTW…my traditional M.D. thought my RT3 was just fine. See an integrative M.D.


What do you recommend in place of NSAIDs? I have pain that I do not think is associated with my autoimmune conditions (hypothyroidism, rosacea, celiac and undifferentiated connective tissue disease). I have five disks in my neck and back that are subluxated, bulging or disintegrated. Most of the time life is good! However, I frequently need to take an Advil in order to fall asleep. Due to the nature of my issues, I really do need an anti-inflammatory to cut the inflammation – right? I am trying really hard to follow the autoimmune paleo diet and I do see some improvements. I hate to sabotage it by taking the Advil (if I am going to cheat, it should be more fun :) ). Sometimes Deep Blue (a doTerra blend) will get it but not always. What is friendlier to the gut? A muscle relaxer seems to slow things down; but, is it a better choice than NSAID? I am very hesitant to take narcotics or other prescription pain killers. I am also allergic to codeine and Lortab. I appreciate any advice. I cannot say thank you enough for your website! It has been so helpful! I appreciate your science behind your solutions. Thank you for all of the care, time and research that you put into it!!

You are saying ” If you have Grave’s Disease or Hashimotos Thyroiditis, you must also avoid goitrogenic foods”. I heard in the last Hashimoto summit that this is a myth that is very popular on internet sites but actually when you go and dig where’s the paper that supports this – then you can’t find one. I was wondering if you can back this statement with a relevant paper.

[…] so a sleep study, too. Also, I’ve written before about having a paleoish diet. There’s an autoimmune protocol (AIP) version of the paleo diet I may check out over the summer and see if that helps, […]

I suffer from autoimmune disease (MS) and I’ve spent a year researching how immune system works, and was ultimately able to put my disease under control. I feel great 99% of the time. This article is steaming pile of shit. I eat both grain and legumes and all of your “forbidden” foods all the time in large quantities. “Leaky gut” syndrome doesn’t exist. Food never affected my condition. Stress did. Ask any real immunologist to explain you why this story sucks, I don’t have time to waste on you people.

I have Hashimoto’s, leaky gut, food sensitivities big time, major fatigue (adrenal fatigue). I am on the AIP diet though I have had some sprouted walnuts recently. My inflammation is improved and my gut overall is improved but still having issues. I am extremely sensitive to so many things. For two weeks I didn’t take any supplements because I was preparing for the adrenal saliva test and I think I felt a little better. As soon as I began the supplements again, my low back pain started again and my fatigue is worse than ever. I am getting sick of meat, my HCL levels are extremely low as I got up to about 10 HCL without any burning but then they started getting stuck in my throat so I quit and started using ACV which helps. I just don’t know what to do at this point. I have an acupuncturist who is pretty knowledgeable but I really do need some guidance to repair the leaky gut. I am waiting for my genetic test to return and am sure I have the MTHFR gene. Help!

I realize that even cooked sulfur veggies…Brussels broccoli etc causes migraines for me and bloat. I think some of us with MTHFR and detox issues may be challenged to eat high sulfur veggies. Its hard as heck bc starch triggers no sweet pot winter squash any form of grain etc.., and now no sulfur veggies or ferments…. I’m at a loss. I’m eating some lettuce and cukes but know that’s not good long term.

Undoubtedly you are very knowledgeable and kind for providing all this wonderful info for free to help people but I find your use of a lot of medical terms makes it very hard to understand the basic info. I often have to research words then come back to your page and try to apply those definitions to barely grasp what you’re conveying. For eg, I was completely lost in your explanation about why egg whites should be omitted from the diet but I’m going to stop eating egg whites anyway. I’m very confused and overwhelmed

I’m a small man and with all the diet restrictions, I’m wasting away. to begin with, I can’t eat most cruciferous veggies and the veggies you said to omit are what I was surviving on. i eat fish, and some chicken but can’t bring myself to eat meat or organ meat and with potatoes, brown rice and oats out the picture, I have no idea what to eat. is there a way for you to simplify all this? Thank you

This is SO depressing. I’m a vegetarian, and no that is not changing.
SO, basically I can live on greens with a little coconut oil.

I get confused on the grains and legumes. So after my elimination period, I can’t reintroduce brown rice? Or gluten free flour blends? I miss brown rice.
And the only thing I’m really craving on this AIP diet, is chickpeas, but now that seems to be out the pictures. No more chickpeas? Is that accurate? As a vegan, that’s one of my main staples.

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