The Paleo Autoimmune Protocol – An Elimination Diet for Autoimmune Disease

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Disclaimer: Before we delve into the specifics of the autoimmune protocol (or AIP), I would like to make a couple of things clear: First, I am not the creator of this protocol. I originally came across the idea of it as Dr. Kharrazian’s autoimmune hypothyroidism diet as well as through the work of Robb Wolf and Chris Kresser. Second, Sarah Ballantyne, PhD and author of The Paleo Approach is to be credited with doing all of the deep research and refining the protocol as it is known today. Since she is a scientist and very well qualified to be making the calls on the protocol given her deep research and extensive experience. What I have written here barely scratches the surface compared to the amount of information you will find on her website, The Paleo Mom and her book, The Paleo Approach. My recommendations here are the same as what Sarah advocates on her website and in her book, because lets face it – she is the expert!

What is the autoimmune protocol?
The autoimmune protocol is a version of the Paleo diet (no grains, legumes or dairy) where a person also avoids the following:

-seeds (including cocoa, coffee, and seed-based spices)
-nighshades (tomatoes, potatoes, eggplant, peppers, and the spices derived from them)
-excess fructose (more than 20g/day)
-potential gluten cross-reactive foods
-non nutritive sweeteners (including stevia)
-emulsifiers, thickeners, and other food additives

For some awesome print-out guides with lists of what to eat and avoid, click here!

What is the theory behind the autoimmune protocol?
The autoimmune protocol was derived from the recent research indicating that autoimmune disease stems from a problem with intestinal permeability (or “leaky gut”), instead of the commonly assumed infection that resulted in autoimmunity. Simply put, when a person has leaky gut, irritation in the gut lining causes the tight junctions in the intestinal barrier to let unwanted molecules (food, toxins, bacteria) into the bloodstream. All the foods avoided on the autoimmune protocol are those that have been shown to irritate the gut or cause increased permeability in the gut. If you want to dig in to the science behind the autoimmune protocol, check out Sarah Ballantyne’s book – The Paleo Approach.

Do I have to go on the autoimmune protocol forever?
Some people feel best when they stick to the autoimmune protocol 100%. For some, the relief of symptoms is worth the difficulty of adhering to the diet strictly. Some people use the autoimmune protocol as a type of elimination diet by doing it for a period of time (I recommend 1-3 months) and then reintroducing foods slowly to test them. Some people are never able to tolerate certain foods on the excluded list, but may be able to tolerate some of them in small quantities. All of these things are dependent on how the person feels – obviously if a person is very ill, and being on the autoimmune protocol makes them feel better, they will do their best to stick to it. On the other hand, some people do well on the autoimmune protocol for a period of time, and then through the reintroduction of certain foods find their tolerance limit of them. This person may be able to stick to the autoimmune protocol most of the time, never eat some of the restricted foods but be able to tolerate some foods on the list on occasion and still feel good in the long run.

For more information, please check out this post on Sarah Ballantyne’s website. She goes into great detail about the whys of the protocol, foods that people are commonly confused about, and which foods someone who is attempting the autoimmune protocol should include lots of in their diet for maximum healing – all extremely important facets of this process. I am not trying to reinvent the wheel, so I am not reposting that information here. Go dig in on her site and then come back looking for recipes and inspiration.

About Mickey Trescott

Mickey Trescott is a cook and one of the bloggers behind Autoimmune Paleo. After recovering from her own struggle with both Celiac and Hashimoto’s disease, adrenal fatigue, and multiple vitamin deficiencies, Mickey started to write about her experience to share with others and help them realize they are not alone in their struggles. She is a certified Nutritional Therapy Practitioner by the Nutritional Therapy Association, and is the author of The Autoimmune Paleo Cookbook, a guide and recipe book for the autoimmune protocol, and AIP Batch Cook, a video-based batch cooking program. You also can find her on Instagram.


  1. Heather says

    I notice cashew isn’t on the Foods to Avoid list and I have access to fermented cashew products. I also don’t see cashews on the Foods to Include list either. Can you tell me if cashews are “legal”. Thank you. Heather

    • autoimmunepaleo says

      Hi Heather,
      It is best to avoid cashews while on the elimination diet because they are a nuts. It does not matter if they are fermented or not. Good luck!

      • Sarah says

        I see that potatoes are on the list of foods to avoid. Does this include sweet potatoes? I was told that was alright! I have Graves Disease and was on this type of diet for almost a year, 3 months very strict. I was however able to eat gluten free products and nuts (just a little daily). My T4 and TSH did get better in February but has progressively gotten worse. I also have a heart disease so had to get back on meds since it does cause heart rate increase.

        • says

          Hi Sarah,
          No, white sweet potatoes are not in the nightshade family. I hope that you are able to find some healing through changing your diet!


        • says

          You are right, they are not true nuts, but they are not included on the elimination diet nonetheless.

          Hope it helps!


  2. Marianne Willis says

    I am very upset to hear that you have to eat meat on the paleo diet for protein. I was watching Dr. Oz one day when a doctor who has done a lot of research on Alzheimer’s, stated that meat and fish, as well as iron, copper, zinc, & high fat are contributory. I am not a vegan, but eat a primarily vegetarian diet and get my protein from beans, legumes etc. Is one supposed to trade an auto-immune disease for Alzheimer’s?

    • autoimmunepaleo says

      Hi Marianne,
      I was pretty upset when I found out, as I had been vegan for 10 years. All I can say is that opening my eyes to the fact that maybe all of the doctors and researchers that I had listened to as a vegan could have been wrong or had a bias when they were presenting their work. Through the work of people like Diane Minger ( I have found their studies to be flawed. Additionally, I have experienced incredible healing eating this way. Ultimately, you should do what feels intuitively right for you and not listen to what someone on Dr. Oz says. These experts have agendas, reference research that is flawed and are constantly contradicting themselves. I have not seen a study that shows that a diet without processed, refined foods and anti-nutrients such as beans and grains causes alzheimers – if you know of one you can send it my way!

      • says

        Very well said. Indeed too many agendas which causes too much confusion. When you realize that and follow your intuitive instincts while watching/listening to your body then you will experience true healing.

    • Dana says

      Actually, Alzheimer’s is thought by cutting-edge researchers to be a form of diabetes, and you’re more likely to give yourself that disease on a high-starch, high-sugar diet (even natural sugar) with all plant fats and no animal foods at all. You need iron and copper and zinc and fat. I don’t know what Dr. Oz is smoking but I don’t trust him as a nutrition advisor, and I’d view anyone who appeared on his show with extreme skepticism.

      Also, you don’t just get protein from meat. You get vitamins and minerals and essential fatty acids, some in forms that you cannot find in plants. There is no way I can be vegan because I found out the hard way that beta carotene is no substitute for vitamin A in my body. Come to find out that as much as half the population (according to both a U.S. and a UK study) are in the same boat as me. Given that vitamin A is important in fertility, it’s not difficult to figure out where all the infertility cases are coming from.

      • Rita says

        My mother, who ate no beef or pork, but did eat chicken, fish, salads, brown rice and pasta, got Alzheimer’s disease. My dad, who enjoyed nothing more than a big juicy steak or a plate of bacon and eggs, did not. We have no idea what causes Alzheimer’s. We can observe certain correlations but those are not causes. For all we know the disease is genetically determined and certain lifestyle choices either promote or suppress expression of the genes that cause the disease. One thing is clear: blaming meat eating for every disease under the sun is simply spurious.

  3. Amanda Evans says

    I see that coffee is excluded in the Autoimmune Paleo diet. Is it just coffee or caffeine in general?Have you heard of The Clean Gut Programby Dr.Junger? I was wondering what your opinion is?
    Thanks for everything you post, I have learnt a lot from you! I have Crohn’s and Hashimoto’s and the last 14 year’s have been a huge journey but having just discovered Paleo fairly recently I finally feel like I know how to help my body!

    • autoimmunepaleo says

      Hi Amanda, coffee is not allowed because it is a seed. I also recommend avoiding caffeine altogether, because it can exacerbate Th2 dominant autoimmune conditions and is hard on the adrenals. At least give it a break for awhile, and then try again to see how it affects you.

      I haven’t heard of the clean gut program – is it similar to AIP?

      I wish you continued success with Paleo and AIP!

        • says

          Lauren, green tea is OK but be warned it is an immune stimulant and can cause flares in some people. Caffeine is not specifically not allowed, but it also has an effect on the immune system. It is important to be cautious of these things, while they are not specifically avoided on the autoimmune protocol.

          • CA says

            Green Tea, as also other teas and coffee, blocks the uptake of much needed minerals, according to iron disorders institute. As already stated, we need minerals and natural fats that solidify in the frig. These are vital to our adrenals and thyroid etc. Alzheimers is related to heavy metals, neurotoxins, which I believe are assaulting our gut linings, having a heavy hand in intestinal permeability to begin with, causal. Those ” experts” like to say that the very things we truly need are the causes, when the opposite is true. The thyroid cannot do its huge job without iron, copper, zinc, magnesium, manganese, selenium, potassium, calcium, the whole long list of minerals. The thyroid regulates the heart, heartbeat, etc. Those minerals are essential and mandatory for life. Our adrenals cannot produce the hormones without healthy natural fats (cholesterol). We have been very lied to. This reply is largely to the above vegan who has listened to the mainstream. Thank you to all the paleo ” moms” , cooks, researchers, and bloggers, that have brought this lifesaving information to the light of Day, freeing us from the lies. Thank you.

  4. Lisa Vincent says

    What if you don’t have leaky gut? I have been tested for leaky gut via an IgG test and it was negative. Should I still follow an AI protocol for an autoimmune disease? Thyroid disease runs in my family, so I’m assuming that’s where I got it from.

  5. samantha says


    I have been coeliac for two years and last week was diagnosed with endometriosis and fibromyalgia.

    I stumbled onto your website and am wanting to start the autoimmune protocol diet. Is it really necessery to exclude eggs? They are used so much in my gluten free foods that i make so it’s going to be extremley hard. Is there an alternative that could be used to bind? Also do you suggest i also incorporate the FODMAP diet?

    Thank you


    • autoimmunepaleo says

      Hi Samantha,

      It is absolutely necessary to avoid eggs for the elimination phase, as there is a component in the egg white (lysozyme) that can be problematic for those with autoimmunity. I would recommend sticking with whole foods, like pastured meats, and fresh fruits and vegetables while on the elimination diet instead of making treats or replacement foods. I don’t recommend incorporating low FODMAP approach unless you are certain you have SIBO – it is very strict. Good luck!

      • samantha says

        Thank you so much for your response, i really appreciate it. Im looking for lunch ideas beside salad! And was wondering if ham or turkey meat would be suitable or not due to processing? Sorry…im new to all of this but thank you so much for your wisdom :-)

        • autoimmunepaleo says

          Samantha – it depends on the processing. I would look into the brand you are considering purchasing and research how the process the meat and with what ingredients. The only cured meat I have personally used is prosciutto.


        • Elle says

          Chia seed is used as a substitute for egg when baking, however it sounds like that might be off limits for the time being.

        • CA says

          The parasites that remain in pork are a problem. No matter how it is cooked, cooking is not fully effective against all the parasites. The job of hogs is to clean up the land, just as the job of shellfish is to clean up the oceans, and when they are allowed to do that in high numbers, they do a wonderful job of it. The fresh waters also have their ” vacuum cleaners”: catfish and other bottom- feeders. They are here to ingest what is harmful, in protection of mankind and the earth. They are not here to be eaten: When we eat ” vacuum cleaners”, we are ingesting all the toxins and heavy metals they eat. We should let them do their jobs. That is the only way they can actually serve us, by cleaning up the earth. This is their special design.

  6. Richard says

    I’ve had celiac for four years and have still been feeling fatigued even on the glute free diet so I am now switching to the AIP. I’m getting conflicting info on dairy, especially cheeses, which is not part of the list. Should cheese be part of the overall list? Or a speculative addition to the list? I’m kind of perplexed.

    • autoimmunepaleo says

      Richard – dairy is not allowed on the autoimmune protocol.

      I also have celiac, and did not find relief until I found out about other foods that were causing my autoimmune symptoms to flare up.

      Good luck!

  7. Richard says

    Oooooops, never mind. I missed the initial parentheses concerning dairy. Sorry about that! I’m clear now.

  8. samantha says

    Thank you :-) im relieved prosciutto is ok tho! Is honey ok as there seems to be conflicting results too. I need a substitute for sugar!

    Thanks for your help :-)

  9. Ellie Wylie says

    Hi there, I’m wondering if Balsamic Vinegar is allowed on the diet? Also, if pure homemade dark chocolate is? And last thing, is it okay to drink store bought Kumbacha? I believe it’s GT’s Kumbacha that is sold in stores. Thanks!

    • says

      Yes, but you must be careful of the source. Some balsamic is aged in barrels that are sealed with wheat paste. I would call the company or check the bottle to see if they are gluten-free.

      Chocolate is not allowed. Kombucha, even storebought is fine. Good luck!

  10. Cheryl says

    Is there any way to pay for this besides Paypal? I am just beginning my journey and would love to have this great resource! Thanks!

  11. AmyLou says

    Wow! I feel like your website is a Godsend and plan on ordering your book! My reaction to foods seems to show itself in swelling around my neck. I also have thyroid issues, and I believe I’m Hashis as well. I have severe leaky gut, and the list of foods I can eat has been getting shorter, and until I found you I couldn’t make any rhyme or reason out of it. I have one question though, I can not tolerate dairy that has been pasteurized… However raw goat milk in small amounts doesn’t bother me. Given the probiotic benefits would raw milk and raw goat kefir be acceptable in the elimination diet if the good bacteria helped my leaky gut??

    • says

      Hi Amy,
      Unfortunately, dairy of any kind is not allowed on the elimination diet, even if it is raw. I would make sure to leave it out and do a systematic reintroduction once your symptoms lessen. Good luck!

  12. Paul says

    Hi Mickey!

    I’ve been reading your blog for a couple weeks now and it has been immensely helpful. I have been dealing with scalp psoriasis for close to a decade now and it has been such a burden.. I have a couple questions I was hoping you could answer. Would smoking marijuana sparingly impede the healing process? I smoke a little before bedtime to help me fall asleep, I have found this to be the most effective natural remedy for my insomnia. Also, would coffee enema’s be advisable? I’ve read that they are superb for helping the liver detoxify. Thank you.

    • says

      Hi Paul,
      I don’t know about the marijuana, I know a lot of people with chronic illness use it and I haven’t heard any negative reports in relation to autoimmune disease. I can’t really advise you on that one, but if you are doing everything else and still no relief you might try to go without it for a time to see if it has an effect. I am not a fan of enemas – your liver will detoxify enough with the diet change as it is. You can do some other complimentary detox therapies, like using a sauna, dry brushing, or epsom salt baths, but I would steer clear of enemas. Hope it helps!

    • CA says

      Paul, I recently came upon a sleep- consultant’s teaching on breathing from the diaphragm both for day, and for its great benefit to sleep, and as well, specifically, also for getting to sleep. Boy, oh boy, what a huge difference it makes! After years of difficulty, now I can drift right off to sleep and stay asleep. He explained how it causes the entire body to relax, whereas breathing from the chest causes body- wide tension. My body attests to his knowledge, definitely worth reading more from him, and breathing that way. Helps the nervous system too. I also remember reading that weed is inflammatory and overuses our minerals, which we are generally short on to begin with.

  13. AnnaO says

    Lovely site! I have multiple food sensitivities and CFS. My diet is similar to the autoimmune protocol and I definatley will get your book. A cookbook where I can have almost all the recipies! Unheard of in my world, so thank you! I was wondering, though, about winter squashes/pumpkins, are they ok? If not, why? Thank you :)

  14. Shea says

    Hi Mickey,

    In conjunction with general paleo, is AIP a eating lifestyle or a an elimination/reintroduction diet. I am assuming Flaxseed is out of the question. Here is a question I have and I am sure others as well: on a tight budget, is it better for me to eat conventional meat and farm fish or stick to a plant based diet and occasionally have grassfed food and farm fish. For the past few months I been on a plant based diet no meat.

    • says

      Hi Shea, it is an elimination diet and a lifestyle – you do the elimination diet to find your food triggers, then continue to eat that way. I did my original elimination diet for about 6 months, and I have been eating that way for another year and a half. I have no plans to stop eating this way, as I feel fantastic. Whenever I reintroduce something I am obviously not ready for yet – mainly nightshades or grain, I get a return of my symptoms and it is not worth it.

      Flax is a no. If you are on a budget, I would make sure to include meat, maybe occasionally but higher quality. You may have to make the decision to eat more, lower-quality meat because your body craves those nutrients, or less higher quality meat. I would look into purchasing offal from a local farmer or farmer’s market – often this is the lest expensive cut of meat and it has the highest nutrition. I find liver from pastured cows at my market for $3/pound – can’t beat that!

      Best of luck!


  15. Shannon says

    Thank you for posting this information. I have been eating strict paleo for a little over 1 month. 2 weeks ago my blood test showed that I was Vit D deficient, I have since been taking daily supplements. My interest in going paleo was based on the simple fact that I suffer from a few auto immune symptoms that are very disruptive to daily life. The main ones being skin irritations specifically around the mouth (dry, red , pealing), and chronic dry,pealing patches on top of feet/ankle region. The worst is raynauds that I’ve had for 4 years.
    The skin conditions have improved on paleo and with vitamin d supplements but are still present. Raynauds has not improved and as the weather is cooling I am desperate to not have to carry hand warmers 24/7. or get out of a nice hot shower only to have all my fingers colorless and numb.
    I am interested to hear any success stories for people with raynauds and/or eczema after making the switch to the auto immune protocol paleo diet.

    • says

      Hi Shannon,
      I actually have a roommate with severe Raynauds that has been greatly improved by going on the autoimmune protocol, but it has taken her nearly a year to heal. She also has RA, and I have heard accounts of people that have it as a symptom of another autoimmune disease improve with the AIP. Those that have Raynauds without another autoimmune don’t seem to improve. LOTS of people have been helped with their eczema – if you send me a post on my FB page I will put out a post and you will get tons of answers.

      I think it is worthwhile to do the elimination diet and find out your food sensitivities, even if you don’t know if your Raynauds is related to an autoimmune disease of not.

      Best of luck to you!


  16. says

    Thank you for the great info! I have been on the AIP and using the cookbook for about 10 days now and have noticed significant changes in my digestion which is making a huge difference in my energy. A question for you: do you have a suggestion for a protein powder? I find my body is not wanting a big breakfast and I have been juicing veggies but need some protein. Hemp? Pea (although it is a legume)? And do you know what the protein count is in bone broth, generally speaking? Thank you! – Saivite
    (Ps. I made the Pumpkin Spice Cake for Thanksgiving and it got rave reviews :)

    • says

      Hi There! That is great news!

      I don’t recommend any protein powder on AIP. Hemp, pea, and others are all made from unallowed foods on the autoimmune protocol, and are also highly processed. I would strictly avoid them. You don’t necessarily need to eat a big breakfast, maybe you could make some meatballs out of any of the sausage recipes in the book and eat one or two with your juice in the morning?

      Bone broth might be a nice idea but I don’t think it would be enough to sustain you. I would just focus on a smaller portion of protein in the morning, and increase if you can. You may find your morning hunger improve as you continue eating this way. Best of luck to you!


  17. Christin says

    Re: the above comment on adding protein… I have been using grass-fed gelatin (this one, which does not gel: ) in coconut milk / greens / avocado and date smoothies in order to keep me a little more satiated. Also add small amounts of other fruit on occasion. Any issue with this gelatin?

    Enjoying your site… have RA and have had issues with many meds. Looking to ameliorate symptoms with diet as well. Some success with a more ‘paleo’ approach. Hoping I can manage this stricter way of eating. As you say, the consequences of eating things that make you feel ill is a great deterrent to doing so, and makes the whole restriction-thing more attractive! 😉

    Best, Christin

    • says

      That gelatin is fine, and although I haven’t used it I hear it is nice for cold application.

      I’m wishing you the best with your RA!


  18. Angela says

    Is there a “fructose” chart available online? I would like to know the fructose content of foods so I don’t exceed the recommended amount (max 20 g/day).

  19. Teresa says

    Hi Mickey,

    I bought your book a couple of weeks ago with the intention of doing a strict 30 AIP trial. My dh even agreed to try paleo along with me (he was still eating eggs, nuts, tomatoes, etc.). After only a day or two on paleo muscle twitches and heart palpitations he had been having for years went completely away and for the first time in ages I didn’t have major PMS migraines. Unfortunately last week I came down with the flu and with me too ill to cook or tell my husband what to cook we both went back to our old eating patterns and we’re both feeling pretty crappy again. We’ll be out of town about ten days for the holidays and to be perfectly honest I don’t see us being able to be strictly paleo until we’re back home. We plan on just doing the best we can and try not to stress about it too much. Anyway, when we get home I have a couple of days before I have to go back to work so I’m planning on doing a bunch of batch cooking so we have the freezer stocked with AIP friendly foods. I’m just wondering if I should do some kind of detox before getting back on the AIP or just dive right in to the AIP?

    I also have a book question – when I put it on my kindle it showed up as a document and not a book. I can go from page to page, but none of the links work. Any idea what I did wrong?


    • says

      I don’t think you need to do any sort of detox to go back to the diet – just switching back will cause you to detox enough! I would transition back however you like – if you don’t have a problem starting 100%, go for it, otherwise it is fine to ease your way back into it.

      As far as the book on your kindle, that is frustrating, and since I don’t have a kindle I don’t know the answer. I do know it is possible to have it function fully as an ebook. I would contact Amazon customer support with your model and ask them how you can get the book to work properly on their device.

      Good luck!


      • Teresa says

        Hello again,

        I checked on the problem with my Kindle and apparently I need to download it again, but the link has expired. Is there anyway it can be emailed to me again? I think what happened is that I downloaded it on my desktop, then tried to transfer it to my Kindle when I should have just downloaded it directly to my Kindle. I probably should have found a kid to do it for me instead of trying to do “technical computer stuff” myself – lol!

        Any suggestions for road trip and AIP friendly foods? I plan on taking fruits, veggies and cans of tuna, but beyond that I’m drawing a blank. I had planned on waiting until we got back to get back on track foodwise, but I’m feeling so crappy it just doesn’t make sense to cause myself any more damage.


  20. marcia says

    Hi Mickey,
    I have been doing paleo diet for month and have been feeling a lot better, I have lupus, RA, fibromyalgia, GERD and hypothyroidism. My question is I have been on acid blockers ie nexium for 25+ years when I miss a dose I’m sick all day. Any thoughts of how to get off them? I can’t wait to get your book, I’ve just been eating plain meat and veggies.
    Thank you, Marcia

    • says

      I’m sorry to hear of your issue with stomach acid. Sometimes when people are being treated for excess acid, it is because they actually have low stomach acid, and the long-term solution is to build up your natural acid. This is something I would work with your doctor on. I’ve written an article about it here:

      Make sure you don’t self-treat with something like this – you do need the help of a qualified functional medicine practitioner on this one!

      • Marcia says

        Hi Mickey,
        Thank you for your great advice! I as wondering if organic beef, chicken, and pork are ok? I’m having a hard time finding grass fed and when I do it’s from $10.00 to $25.00 a lb.
        Thank you,

        • says

          Yes, organic is fine. I suggest looking at to find a farm nearby where you can find meat in bulk–it is quite expensive purchased at the store, but you may find it more affordable to buy in bulk and store in a deep freezer.


  21. Ann says

    Hi Mickey,
    I have had alopecia since I was 19 (now age 47) but no other symptoms or autoimmune issues except thyroid antibodies once or twice in the past five years which I have successfully lowered. I have followed the GAPS diet for almost 3 years, with no affect on my hair growth. It has been suggested that alopecia may have an autoimmune component, but no certainty. Do you think this diet might elicit hair growth? or do you know of anyone who has tried it?
    Many thanks,

    • says

      Hi Ann,
      This would be a great question for the facebook community, and I will ask it in the coming week. Stay tuned for responses – I think it is definitely worth a try of the autoimmune protocol; it eliminates some additional foods that you might find problematic. Good luck!


  22. says

    Hi Mickey,

    I’ve done Paleo for a while now and have not seen a lot of weightloss like I had hoped with my busy CF schedule. I was diagnosed with hypogylcemia, insulin resistance, PCOS, IBS and a goiter since I was 13 and struggling with my weight since then as well. I love spices, eggs and cooking so the nightshade elimination makes me really nervous. I also use grass fed whey since I work out so strenuously. However, I have horrible skin eruptions continuously down my back, legs and butt (tmi, I know). I have bouts of fatigue almost daily. I feel better since Paleo but I feel like something is missing that I’m not having as much success as I was hoping for. I’m gluten intolerant and was miserable being vegan so that didn’t work. I’m wondering if I need the AIP to see a difference in my weight, skin and energy. What do you think based on what I’ve shared?

    Thank you!

    • says

      Hi Candy- you never know until you try! I really believe in a Paleo style diet for optimal health and troubleshooting complicated issues. I don’t know if you need to do full AIP to start, but I would definitely try Paleo and see what it does for you. Good luck!


  23. Kristen says

    Hello Mickey,
    I have rosacea and acne that I ended up seeing a naturopathic doctor for and he had me get blood drawn for standard food panel testing for allergies/intolerances. I reacted to a very high number of foods but I tested negative for crohns and celiac, so was diagnosed with leaky gut. The results showed high igA and igG for dairy, yeast, grains, legumes, most nuts, and eggs but also lamb, pork, turkey, beef, and most fish/shellfish. The beef also had a high igE level, which I believe is marker for “true” allergy. Do you know much about the blood allergy testing and it’s accuracy? The autoimmune protocol as well as other diets I researched on healing leaky gut stress importance or beef broth, gelatin, liver, and importance of red meats and fish over large amounts of poultry because of omega 3:6 ratios. I guess I’m confused on if I should start elimination diet with just chicken and halibut and sole since I tested ok for these or include other meats as well. I don’t think I’ve ever had a reaction to red meat, however I don’t want to delay my progress. Any thoughts or advice would be greatly appreciated! Thank you!

    • says

      Hi Kristen,
      I don’t put much stock in those allergy tests, as they have been shown to be pretty inaccurate. Even by allergists, the gold standard for pinpointing food allergies and sensitivities is the elimination/provocation challenge. If you want, you can start by avoiding non-AIP foods + what came up on your allergy test, and then planning your reintroductions from there. I do agree that is a pretty big list though!

      Good luck!


  24. lissa says

    Hi Mickey,
    This may be redundant but is, evening primrose and borage oil ok to supplement with on the AIP even though they are derived from seed ? Also, not sure what your answer was on small amounts of raw honey. And again, storebough Kombucha ( like Synergy) is is really ok with it ’s trace amounts of sugar and alcohol or is it great for breaking down meat etc… thanks so much

    • says

      I would avoid the seed oils while on the elimination diet, although they are not likely to be problematic. Small amounts of raw honey are fine. Kombucha is also fine.

      Good luck!


  25. lissa says

    PS .. I am surprised to see dates and dried fruit on the ‘to include ‘list since they are so high in sugar. ( plus I have a terrible time not eating a whole box of dates when I get craving and want a treat). Are they for everyone ??

    • says

      The list isn’t about foods that are low in sugar, it is about foods that have been shown to exacerbate leaky gut. While I agree with you on the sugar, dates are fine as long as you tolerate them. I wouldn’t say they are for everyone, and if you have self-control issues with them, certainly don’t keep them around!


  26. Theresa says

    I tripped over your site – from empowered sustenance – I am starting this! I have Celiac Disease – been diagnosed for over 10 yrs. My villi finally healed about 2 yrs ago, I also have Microscopic Colitis – the inflammation has yet to settle – I have never had relief from the runs. I am hoping to see improvement! My only concern or issue is how hungry I get, sometimes I get nausea… but I am sticking with this! Is there a cleansing that is taking place in my body? My runs are still watery (were prior to diet, as well as undigested foods). I was eating a high grain, dairy and egg filled diet – as well as a lot of processed foods – maybe my body is in shock! lol thanks for all your information!

    • says

      Hi Theresa,
      I’m sorry to hear of your ongoing issues, but happy you found me here! Have you been tested for any GI pathogens? You want to rule that out before tweaking too much with diet, otherwise things will get very frustrating. Some do find that transitioning to a diet without grains, eggs and dairy is helpful to managing your inflammation. Wishing you the best of luck!


  27. jangle says

    Many of the things on the avoidance list are highly recommended through other research for Rheumatoid Arthritis, namely specific nuts and nightshades.

    Do you have suggestions for items that replace the nutrients or benefits attributed to the items your list recommends to avoid?

    • says

      Have you seen the book The Paleo Approach by Dr. Sarah Ballantyne? She has done the most thorough research on the topic, and has studies to back up the protocol. I know from working with people that nightshades are one of the most common triggers for those with RA.

      The autoimmune protocol is an incredibly nutrient-dense diet, if not the most nutrient dense diet. As long as you are eating a variety of foods, you don’t need to add in anything to make up for missing nutrients.


      • jangle says

        Thank you Mickey! I’ll pick up a copy tomorrow (if I can find it local). My husband was dx’d with RA about 5 years ago and told he would most likely be in a wheelchair within the first year of diagnosis. We already ate healthy-ish, but once he started his meds (handfuls of pills and Humira injection 2/mo) I started doing more research on the side-effects of it all.

        Until going Paleo, he was a human pill-box. Since going completely paleo he takes meds when necessary and has gone as long as 6 weeks without injections. HUGE improvement.

        Of course, I would prefer to see him off of all the pharmaceuticals if possible, especially after having another relative that has RA recently dx’d with pancreatic cancer (a common end result side-effect to a number of the meds my husband also takes).

        Guess you could call me “Desperately Seeking Solutions” :-/

  28. Katie says

    Did you heal your auto-immune disease completely or are you in remission? Do you take pharmaceutical drugs? For my lupus I take an anti-malarial (hydroxychloroquine aka plaquenil) and coumadin (the blood thinner). I’ve never seen a homeopathic or natural doctor but I would really like to. Anyway, my main concern is, do you think it’s possible to eventually get off chemical drugs completely and just control an auto-immune disorder through diet and natural medicine? Obviously, I’m not going to just go and quit these drugs at the drop of a hat, but I am extremely curious as that is my ultimate goal.

    • says

      I haven’t had symptoms of my autoimmune diseases in over a year. I do take synthetic compounded thyroid medication, and if my labs ever indicate that I don’t need it anymore, I’ll drop it, but I am not trying to be a med-free hero. I think it is important to work with your doctor to make sure that if you make any changes, you do them safely. Some are able to go off of meds, others live well with a combo of meds and diet. Good luck!


      • Sarah says

        What doctor will prescribe synthetic compound thyroid meds? I have Graves Disease and have to take methymezole.

  29. Lissett says

    My concern about this autoimmune paleo diet is that it seems to be focusing on hypothyroidism. I’ve been placed on a strict vegan diet for the past 3 months and I’ve been able to be off my meds for the past month. I would do anything for a piece of meat and bacon at this point so I was wondering if this diet works for hyperthyroidism as well?

    • says

      Lissett, the autoimmune protocol focuses on all autoimmune conditions–a lot of talk about hypothyroidism, because Hashimoto’s is the most common autoimmune disease. Personally, I do not believe vegan is a good diet for autoimmune disease–I was one for 10 years, and my health has never been worse. There are many with graves who are using AIP to manage their condition. You never really know if it will work for you until you try the elimination diet. Good luck!


  30. Kaitlyn says

    Do you have any recommendations for vegetarians on the protocol? I am just getting into my research phase but I am already disheartened by the focus on meats and fish. As it is, I feel like I am undereating despite constant weight gain…

    • says

      Kaitlyn, According to Sarah Ballantyne it is not possible to do AIP without meat, but it is possible if you are willing to eat a lot of fish and seafood. I don’t recommend trying the protocol without these animal foods, it is not nutritionally balanced.


  31. Paloma says

    Hi Mickey,

    Im so glad I found your website.. Ive had so many health issues lately that Ive been seriourly thinking of changing my diet, and this post was precisely what I needed. Thanks a lot!

    I wanted to ask if there is the possibility of taking some supplements during the elimination diet, like cod liver oil for example. Thanks again!

    • says

      I think fermented cod liver oil is a great supplement for taking during AIP, and really I think of it more as a food than a supplement. You might want to work with a practitioner for some other recommendations, but generally probiotics and magnesium can be helpful for some people.

      Good luck!


  32. Paloma says

    Sorry I forgot to ask: is tea allowed in the diet? Or how could I substitute my very needed morning cup of coffee?? Thank you!

    • says

      Paloma, yes tea is fine! You may not want to go too crazy on the caffeine though as it can weaken the adrenals. Good luck!


  33. Adriana says

    i have gallstones and i have been doing this diet for sometime, i have had lots of improvement and my gallstones have decreased but i still have two big ones in me that don’t seem to be dissolving, should i take on a liver cleansing diet?

    • says

      I recommend working in conjunction with a qualified medical practitioner on this one–I do not recommend any liver cleanses to dissolve stones without a professional’s supervision!

  34. Rachel says

    I’m just about to start the 2 weeks (is that how long I should do it?) of AIP/elimination diet. I have a few vague symptoms and doctors have just told me to lose weight. I’ve been trying to do that for at least 20 years (since my teens) and nothing seems to stick, I’ve lost and gained 25+kgs (55-60lbs) about 6 or 7 times. I’m now experiencing some joint swelling and pain, fatigue (worse if I exercise), some skin issues, weird things are happening to me when I’m ovulating, permanent pms, headaches (constantly feel on the verge of a migraine with eye pain), sinus problems, and some other things. I haven’t had my own doctor for a few years now as in my town they seem to come and go a lot so I generally just see whoever is available. I’ve recently had blood tests for iron deficiency, thyroid and a few other things – just waiting for the results.

    I’ve decided to try an elimination diet just to see if food sensitivities are causing my problems.

    My question is: How do I reintroduce foods in a systematic way to see how they affect me? Do you have a post about that?

    Thanks very much

  35. Sterling Scoville says

    Do you recommend easing into this, or jumping in whole hog? There are so many foods to be avoided, I’d like to give myself the best chance to do this right.

    • says

      Whatever works best for you and where you are at now. I have seen people do it both ways. Its better to ease in than not try!


  36. melissa says

    Hi there. I have been expriencing autoimmune-like symptoms for 7 months now and doctors cannot figure out what is wrong. I am in constant pain in my joints, extrememly fatigued and am experiencing nuerologisal symptoms. My naturopath did testing which highlighted problems with the nervous system, digestive sytem and endocrine system. I cut out gluten ( i rarely had it before) and food sensitivies 2 months ago and I have been on the AIP for a month. I had one good day the day after i started and since then my symptoms have gotten worse than before. Do you have any suggestions about how long to stay on the AIP? I was really aiming for 30 days as my goal, and continuuing on in this way is very challenging emotionally if I feel worse and have to work so hard to create my meals. Also, I was wondering if there is anywhere on the web as to how to reintroduce foods properly? Thank you for any help that you can give.

    • melissa says

      I forgot to add that my tummy is bloated and it feels much worse than before I started the AIP. I have lost no weight at all either, which is so surprising since i have been eating so strictly.

  37. Debbie O'Grady says

    Hi Mickey – thanks for all of the excellent information on AIP! I keep seeing these acronyms like FODMAPS, and there was another one that started with an ‘s’ and I’m not sure what they stand for (?)

    Also, I see that you were a vegan at one time and I’d like to ask how you overcame any adversity you may have had initially to re-introducing meat into your diet? I was a vegetarian for 17 years and began eating fish, and then chicken and turkey about a year ago. Now that I’ve embarked on the AIP eating plan to help heal my Hashimotos and long-term digestive issues, I tried bacon for the first time yesterday morning for breakfast, and ate ground beef last night for dinner.

    The bacon unfortunately did not go down well – it got lodged in my esophageous and I ended up having to force myself to throw it up (gross I know!) in order to dislodge it after 30 minutes of it not going down. I’m not sure if I ate it too fast and didn’t chew thoroughly, or if it was a psychological issue with knowing that I was eating a pig (even though I bought ethically sourced peameal bacon).

    The ground beef was O.K. – kind of bland, but I also didn’t season it with anything – just sautéed it with green onions and mushrooms and added some mashed avocado on top. I was very squeamish about the blood inside the wrap when I opened it up – I felt like a vampire – lol! The beef was also grass-fed, organic, free range from a local farm.

    I have a deep love and respect for all animals, so although I know that eating meat is good for me and will help me heal (after many years of eating soy EVERYTHING), I also need to somehow get over that psychological hump of knowing that I’m eating an animal.

    Any thoughts or suggestions on how you did it would be appreciated. Thanks in advance!


    • says

      Unfortunately this is a deep story that I will eventually address on the blog, but it was very hard for me to overcome veganism and start eating this way. I went very slowly, and only ate meat when I could not see it–the more it could be mixed up with other foods, the better. I’ll elaborate how I overcame the psychological aversion on the blog.

      As far as the bacon not going down, it is very common for ex-vegans and vegetarians to have issues with low stomach acid. I treated mine with a practitioner, and found it was much easier to eat meat once I could digest it. I was also encouraged, because eating and digesting it was making me feel better.

      Wishing the best for you Debbie, I know how hard this transition is!


  38. Terri says

    I have had Hashimoto for almost twenty years, I have been gluten free for about 3 years. I am now trying the AIP to help with persistent symptoms. At one point I was tested and am clearly sensitive to eggs. My naturopath said that duck eggs do not contain the same enzyme (sorry, can’t think of the technical term at the moment, lyc??) as chicken eggs. Do you have any thoughts on this?

    • says

      I think what you are referring to is lysozyme, which is present in all eggs. Sarah Ballantyne recommends removing all eggs for the elimination phase. Hope it helps!


  39. Amanda says

    Hiiii!!! Just starting my adventure with foods.Question…I have Lupus. Any evidence that this will work/help me?? This all seems so thyroid based. :( Thank you so much.

    • says

      I happen to have a thyroid condition, but the autoimmune protocol is designed for anyone with an autoimmune condition. Many with Lupus have tried it and seen benefit from finding out their allergies and or sensitivities to food. Good luck!


  40. Kim says

    I have a question.? When I cook/bake zucchini, Yellow Squash, Turnip, Rutabaga, carrots or kale separately and eat them I feel fine. Even if I put a selection on my plate I am fine. But if I make a soup of the above vegetables cooked together I don’t feel right after I have eaten it. I even tried just using water rather than chicken bone broth. Not sure why but I am thinking it has something to do with the goitrogens. I am hoping you will be able to help me understand this. I have been officially diagnosed with Hashimoto’s. After all these years of suspecting it they have finally given it a name now!! I have been on the AIP diet for a while now and I do feel much better sticking to what I am allowed. Thanks for all your help.

      • Kim says

        Mickey, I have read your article. I eat all the goitrogen vegetables. I do believe Rutabaga and Kale are on the list of goitrogen vegetables. I know that by cooking them the goitrogens are less than when raw. Do you think that by cooking them in the water to make a soup and consuming could be affecting me. I steam the vegetables but no problem but when I eat them in the soup cooked together I feel very lethargic after consuming. I find this very strange. Just trying to pinpoint why this is happening and wondering if you have any ideas? Thank you.

        • says

          I’m not sure it is from the goitrogens–they are supposed to be less effective by cooking. You may be reacting to something else. I don’t recommend eating anything that you have a clear reaction to, even if it is an otherwise healthy food. I would avoid those foods cooked that way. Sorry I don’t have more answers for you–bodies are so complex and unique, it is impossible to know all the whys!


          • Kim says

            Thank you for your response. I do find it strange . Hopefully with time it will not be a problem. So for now I just eat them separate!

  41. says

    Green Vibrance? Thinking it would be great for me? If not suggestions?

    I read that you can start with one autoimmune disease in time it may take on and additional form of auto immune disease. Hope that made sense. My understanding you could start with Hashimoto’s. Then as time goes by have Hashimoto’s + Subacute bacterial endocarditis?

    I just found out I have Hashimoto’s a few months ago. My Dr just handed me a script for thyroid medicine. No explaining, or suggestions:) Thanks doc! Would you suggest seeing another Dr, specialist, herbalist, kinesiologist ?

    Purchasing the book:) Thank you for the Food List!

    • says

      I am not familiar with green vibrance, sorry. I advocate eating lots of whole, green vegetables for the vitamin and mineral content, instead of taking supplements.

      Many of us with autoimmunity find that we develop additional autoimmune diseases as time progresses. I have two. I have not heard of the link between Hashimoto’s and the other condition, specifically.

      I do recommend finding a doctor who is well versed in thyroid testing and treatment–those that specialize in naturopathy or functional medicine are usually better then conventional doctors. Good luck!


  42. Carolyn says

    It’s so great to have someone (you!) to ask about this diet protocol! I’ve got lots of issues going on, fibromyalgia, (for 32 years) chronic fatigue, trygeminal neuralgia, acid reflux/ bowel issues and most recently lichen plumus pilaris with frontal hair loss. Yikes. Being that I have NO ENERGY, am often depressed and am siderite g fro total head to toe extreme pain, how does one possibly do all the shopping and food prep to follow this diet? I really want to try it, but it seems so overwhelming. I spend many days in bed. It is very difficult for my mind to focus. Reading and following a recipe takes more mental energy and concentration than I can muster. How do people do it when they are really sick. I realize it may be my only path to getting better, but I’m overwhelmed at the thought of it. Sorry, not to be negative, but I just needed to express my concern. I’ve started and stopped many protocols before. I am seeing a integrative doc who is helping me detox from mold, which recent research has shone may be the root problem for many with fibromyalgia. When he tested me for 3 certain suspect molds, tests revealed I have 10 X’s the “normal” amount. So, after saying all that, let me ask a few questions. 1. I am considering doing some juicing to get some addition super nutrition. I will use both a high grad juicer(pro angel) and a Vitamix (for fiber) and will “chew” each mouthful. Is that ok? Also, I will be out of my normal surroundings, in Fiji, in Oct for 25 days, and I won’t be able to follow AIP very closely there. Should I start now and then just eat as healthfully as I can while in Fiji, and then start up again when I return? Or do you recommend just waiting to start til I get back? I’m wondering if it will be helpful or harmful if I start now, just to stop again on Oct. Thoughts?

    • says

      Hi Carolyn,
      I’m sorry I can’t give health advice because I am not a doctor or medical practitioner. I would advise you to go to your health care provider with your concerns and ask them their advice.

      About doing AIP when really sick–I started when I was housebound and could hardly get up to go to the bathroom, much less shop and cook all the food I needed to get healthy. Somehow I found hope in the idea that I could change my future and as I gained my health back, it got easier.

      I’m not a fan of juicing, why not eat nutrient-dense foods like liver, shellfish, and bone broth for extra nutrition? While I think its important to eat lots of vegetables, the fiber is important, and I don’t think juicing is a better way to consume them. You will have to make up your mind whether or not you will be able to do the AIP while on vacation or not, some have been able to, others not.

      Hope it helps!


  43. Yvonne says

    Hello, I follow the AIP diet. What is your opinion on raw cheese? I haven’t had dairy in over 8 months now, but I saw somewhere that raw dairy could help leaky gut because it contains probiotics from natural fermentation. While it is very hard to find raw milk, almost impossible I should say, organic, raw cheese is easy to find and I would like to be able to eat it if I can.

    Also, what are the supplements you recommend the most, for autoimmune disease? I am taking over 20 supplements right now, however I am hoping in the near future that I can eliminate some.

    • says

      Hi Yvonne,
      If you have been on AIP and considering reintroductions, the best dairy product to start with is cultured ghee. If you can tolerate that, it is OK to move on to butter, and then raw yoghurt, and raw cheese. You need to try them one at a time to assess your tolerance.

      I’m not able to give supplement recommendations without knowing your history–in general I find most people do well with a good probiotic and some magnesium. If you are eating a nutrient-dense, AIP diet with lots of fish, shellfish, and organ meat, you should not need to take a lot of supplements.

      Hope it helps!


  44. Paige Tabor says

    Hi. Can you recommend a protein powder that one can safely drink while on the Paleo autoimmune protocol? The sheer convenience of protein powders is the main thing I miss eating this way (though the benefits completely outweigh any inconvenience). Thank you.

    • says

      Hi Paige,
      Unfortunately the only protein powders are plasma protein and gelatin, which isn’t a complete protein since it only contains a few amino acids.

      Hope it helps!


  45. Barbara says

    Your AIP is heavily based on beef and pork. These are my highly reactive foods. Chicken turkey and fish have been primary source or protein, but very limiting and a bit boring. Any suggestions?

    • says

      Hi Barbara–this is not my version, it is based on research by Sarah Ballantyne (author of The Paleo Approach). Of course, it will not be right for everyone, and you may have to personalize further based on your food sensitivities. You have a lot of options with fish, especially if you eat shellfish! You could also try lamb and bison, or wild game like elk or venison. Hope it helps!


  46. Shannon Hein says

    Is unflavored non-gmo protein powder allowed? I’d like to use it to make pumpkin, banana smoothies. THX!!

    • says

      No, there are no AIP-friendly protein powders. Some people use collagen, but it is not a complete protein.


      • says

        is gelatin not considered a protein powder? I wouldn’t use it as my only source of protein, but it should work for the purpose of making smoothies, yeah?

        i was having trouble while doing smoothies, and figured out it was probably because it was causing me to eat a. more fruit seeds than i normally would and b. it was crushing and breaking up many of those seeds in the process of blending everything, which we’re supposed to avoid to protect ourselves from their internal defenses.

        so i don’t do smoothies any more. i just have bowls of whole fruit and coconut milk, etc. Less work, still tastes great, and I feel better (probably getting a better ratio of foods as a result, too)

        thanks for promoting Sarah’s book. Such a labor of love, so thankful she wrote it!

        • Mickey Trescott says

          Gelatin is not considered a protein powder because it does not have a complete amino acid structure. I think it is great to add to meals/beverages, but not a replacement for a protein rich meal.

          Hope it helps!


  47. Shannon Hein says

    Sorry! Just saw your comment above about protein powders. But would still like your thoughts. Thank you

  48. Spalfva says


    Did you happen to pose the alopecia areata question to your Facebook group? I don’t find it. My 9 year-old daughter is rapidly progressing towards alopecia totalis and I’m quite interested in knowing if anyone has had success with this diet.

    Thank you and kind regards

    • says

      I’ve posted about alopecia many times, but unfortunately things come and go so quickly on FB, and my posts don’t get seen by anyone. I recommend the elimination diet as a starting place for autoimmune diseases of all kind, as they all have a common link in the gut.

      Hope it helps!


  49. Hopeful Healer says

    Hi Mickey–thanks for the compilation of so much valuable info and experience. A veritable treasure trove. I am researching and prepping to begin my elimination phase and wondering if sparkling water is to be excluded?

  50. Julie says

    anybody out there suffering from RA? I am in need of advice. Been on Methotrexate and all biologics including Xeljanz. Ready to be switched to Rituxin IV. I am desperate. Please help. Thank you.

    • Mickey Trescott says

      Many in our community have RA! I recommend Eileen Laird’s website, as a great resource for you. Good luck!

  51. Brian says

    Can you say if indica and/or sativa marijuana eaten with food or infused into coconut oil is AIP friendly?

    I”m curious if eating it would be supportive now that it is legal in Oregon and a local dispensary offers it organically grown.

    Thanks for your time and consideration as always Mickey and Angie!

  52. Rita says

    I’ve been eating Paleo for six years and have a problem keeping the weight on. There’s a lot of fat in my diet (coconut oil and EVOO, mostly) but it doesn’t help much. Now I intend to try the AIP because I’ve been experiencing chronic and unexplained inflammation, but I’m concerned about losing even more weight. I was eating nuts, which I’m now going to eliminate, as well as green plantains which I understand also have to be eliminated. My main starches are sweet potatoes and bananas. What’s your dietary advice for keeping my weight up while doing the AIP? Is it just a matter of quantity? I don’t want to overconsume protein. Thanks.


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