Is the Autoimmune Protocol Right For You?

Eliminating foods from dietIf you think going Primal is restrictive, the autoimmune protocol is downright draconian. But this is by design. The entire point of an autoimmune Primal/paleo protocol is to eliminate all the foods with the potential to trigger any allergenic, autoimmune, or inflammatory responses. That leaves out a lot of delicious foods, many of your favorites—but it can be a powerful way to assess your sensitivities, target the root causes of mysterious health problems, and illuminate a path forward. It gets you back to square one. A fresh start, a wiped slate.

Okay, maybe not totally clean. This is biology we’re talking about. There are no clean slates. Vestiges of past consumption, behaviors, and decisions always remain and affect us into the future. Unless you clone yourself and rear the baby, you’ll always be left wondering “what might have been had I stayed pure…” But this protocol is about the cleanest you’re going to get.

After the elimination phase, after symptoms have improved, you enter the maintenance phase. You marinate in the diet. Allow it to seep into your pores, do its magic.

When everything has stabilized, you can try reintroducing foods. Go slowly. Do one at a time. A little nibble here, a teaspoon there. Allow two or three days before trying the next food. Note any symptoms.

What Do You Eliminate?

Here’s a complete list:

  • Grains
  • Legumes, such as beans, lentils and peanuts
  • Processed foods
  • Seed oils, such as vegetable and canola oil
  • Dairy products
  • Refined sugars
  • Eggs
  • Nuts and seeds
  • Herbs from seeds, like coriander, cumin and nutmeg
  • Coffee
  • Chocolate
  • Dried fruits
  • Food additives, like gums and emulsifiers
  • Nightshade vegetables, such as eggplant, potatoes, tomatoes, peppers and okra.
  • Spices made from nightshades, like chili powder, paprika, cayenne, chipotle, red pepper.
  • Alternative sweeteners, like stevia, xylitol and mannitol
  • Alcohol
  • NSAIDs (not a food, but bad for your gut lining)

Much of the autoimmune protocol will sound familiar to you. Avoiding grains, legumes, seed oils, sugar, and processed stuff in general is easy. You already do that.

But then you start eliminating some other foods you assumed were innocuous, like, for example, dried fruits.

Dried fruits seems extreme—they’re fruits, after all—but who really needs to eat a bunch of apricots, prunes, and dates? They’re so high in sugar and add up real quick. No problem there.

Emulsifiers and gums? Sure, who needs ‘em. I can emulsify and thicken just fine with a trusty egg yolk.

Wait, what? No eggs? How am I going to do breakfast? I guess I’ll have to eat some paleo granola…

Oh, nuts and seeds are out too. Never mind.

That’s cool. I’ll just pour a little extra cream in my coffee.

Shoot. Dairy’s out, too. Black coffee it is!

Why are you making that face? Don’t even—I can’t have coffee, can I?

Hey, that’s fine. I’ve been meaning to get into tea. A big steaming mug of jasmine green tea will be just fine. I might even nibble on a square of dark chocolate while I’m at it. Antioxidant explosion, here I come!

Wait. Damnit. Chocolate is a legume, and legumes are out. No chocolate either.

Like I said, this isn’t easy. After eliminating all the potentially allergenic foods, you’re left with the basics:

  • Meat, fish, and poultry.
  • Fruits and vegetables, except for the nightshades.
  • Coconut.
  • Fruit oils (avocado, olive, coconut, palm) and animal fats.
  • Herbs.
  • Bone broth (or gelatin/collagen).
  • Tea.
  • Vinegar.

You’re removing foods with the potential to irritate the gut and increase inflammation. You’re focusing on “safe” foods that allow the gut to heal (and foods that actively increase gut health).

Why Is This Important?

Some leading autoimmune researchers have proposed that the primary cause of autoimmune pathogenesis is impaired intestinal permeability—or leaky gut. A leaky gut allows proteins, toxins, and other compounds into circulation that aren’t supposed to be there. The body mounts an immune response to the invaders. If the gut stays open, the inflammatory response stays elevated. And if the immune system gets its signals crossed and starts targeting your own tissues that resemble the invading particles, you have the beginnings of an autoimmune disease.

Who’s It For?

1. Folks with autoimmune diseases.

Until recently, the autoimmune protocol was based on biological plausibility, educated conjecture, and a convincing stream of anecdata. It hadn’t been demonstrated in a legitimate study. It did seem to work for many of the people trying it, but it hadn’t been demonstrated in a legitimate study. That changed in 2017 when a study found the autoimmune protocol to be effective against inflammatory bowel disease. 15 patients with either Crohn’s disease or ulcerative colitis were enrolled in the study. On average, the subjects had been ealing with their disease for 19 years. These were IBD lifers.

They spent 6 weeks phasing out all the foods, using Sarah Ballantyne’s great book on the autoimmune protocol as a guide. Experienced Primal eaters could probably phase out the foods more quickly, though the 6 week phase out might be an important part of the total effect.

They spent 5 weeks maintaining the protocol once everything was eliminated and symptoms had stabilized.

11 of 15 patients had total remission. They’d spent an average of 19 years having to map out the nearest toilets whenever they left the house, and all of a sudden they were basically normal. That’s huge. That’s better than any IBD drug.

There are limitations here. 15 subjects is quite low; I’d like to see ten times that many. There was no control group; this wasn’t a randomized trial (which the authors acknowledge). But it’s quite impressive and bodes well for other autoimmune conditions.

Although this was the only study to examine the entire autoimmune protocol, we know that specific foods play roles in certain autoimmune conditions. Gluten-containing grains are a major, perhaps the major offender, since gluten has the tendency to wrench open the tight junctions in our guts (leaky gut) and allow passage of food particles and endotoxins into our bodies where they can trigger inflammatory and autoimmune processes. Gluten-free diets have been shown to help with:

Coffee has a perplexing relationship to autoimmune disease. For instance, it’s well-known to be protective against type 2 diabetes, but appears to increase the risk of autoimmune type 1 diabetes.

Legumes, other grains, seeds, and nuts are all potential triggers of further gut irritation. While I’ve softened my general stance on some of these foods in recent years, they remain problematic for people with avowed food sensitivities or autoimmune conditions.

2. Folks who suspect they have sensitivities to foods.

We eat a lot of food throughout the course of a given day or week. It’s hard to keep track. It’s impossible to keep track, unless you, well, keep track in an explicit manner. And many of us experience odd symptoms we suspect are linked to food—rashes, stuffy noses, itchiness, grogginess—but without the written logs we flail around in the dark. Maybe we’re lucky for awhile. Maybe we nix the right food. But if we don’t know what we’re doing, we’re just as likely to eat the wrong thing, or eliminate too many things.

The AIP lights our way. It provides a baseline. Eat the foods you know are non-reactive and avoid all the foods that have the potential to cause problems. Once the symptoms improve or go away, maintain the protocol for several weeks, then begin adding foods back in one at a time. When the symptoms return, match it with the food you’ve just reintroduced.

3. Curious folks.

As a reader of MDA, you are probably a nutrition geek. You enjoy needing out on dietary minutiae. You like experimenting on yourself. You’re curious about how certain foods interact with your health, and an autoimmune protocol can reveal that. It’s just good information to have, mostly.

Who Isn’t It For?

Most people. Most people don’t have an autoimmune disease and don’t need to go on an autoimmune protocol.

If you’re happy with your diet and how you respond to foods, don’t bother. It will only create unnecessary headaches. Recall that extended dairy restriction may even induce lactose intolerance. Some claim that you were always sensitive to dairy, that your body had learned to deaden you to the subjective experience of the damage being done. I say dairy is a healthy food if you can tolerate it. Inducing lactose intolerance isn’t in anyone’s best interest, if they can avoid it. 

If you’re the type to obsess over food, and you know your sensitivity is a psychological hang-up rather than a true autoimmune response, skip the protocol. It will only feed your obsession and leave you unable to think about anything else but your diet for the duration.

This isn’t for life (probably).

You can certainly eat well and enjoy what you eat on an autoimmune protocol. But the point is not to stay on the diet indefinitely. It’s to wield it as an effective tool, a broad brush that isolates all the likely suspects for questioning. Then you use the scalpel of inquiry to determine which foods—if any—are truly problematic. If you have to keep milk or peanuts or chocolate out forever, so be it. But make sure that’s what your n=1 data is actually saying.

The protocol isn’t a magic bullet. It isn’t a cure. Many other factors contribute to impaired gut health, chronic inflammation, and likely therefore autoimmunity, like poor sleep, stress, lack of exercise, poor relationships, nature deprivation, sun deprivation, and circadian dysregulation. You need to address those too. But diet is a big one, and it’s an obvious target with an established protocol.

Have you ever tried an autoimmune protocol? Are you going to try it after reading today’s post? I’d love to hear your experiences.


About the Author

Mark Sisson is the founder of Mark’s Daily Apple, godfather to the Primal food and lifestyle movement, and the New York Times bestselling author of The Keto Reset Diet. His latest book is Keto for Life, where he discusses how he combines the keto diet with a Primal lifestyle for optimal health and longevity. Mark is the author of numerous other books as well, including The Primal Blueprint, which was credited with turbocharging the growth of the primal/paleo movement back in 2009. After spending three decades researching and educating folks on why food is the key component to achieving and maintaining optimal wellness, Mark launched Primal Kitchen, a real-food company that creates Primal/paleo, keto, and Whole30-friendly kitchen staples.

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87 thoughts on “Is the Autoimmune Protocol Right For You?”

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  1. This article really resinates the reason why I love the Paleo lifestyle

  2. You left out Hashimoto. That means no to Fruits and vegetables period, Coconut or tea and all spices except salt and black pepper. Luckily, animals are safe. It’s not easy going on a strict AIP but well worth it, if you can go into remission and get off the Meds.

    1. No vegetables? I have recently found TPO antibodies and have gone AIP, starting to have less anxiety now and have cut down saturated fat (against my natural instinct) because of high Lp(a) and a blood clot. Would like to know more of your regime…

    2. Since when do people with hashimoto’s have to give up all fruits and veggies?? That would be so unhealthy.

      1. Barb, absurdly not….what you’re saying is not different than those saying that omitting whole grains is unhealthy (-:

    3. Um, according to what research? And even if it WERE valid, would it really be worth cutting all fruits and veg. to manage a disease that’s easily treatable with a simple once-a-day medication with (for most people) no side effects?

      1. “easily treatable with a simple once-a-day medication with (for most people) with no side effects? Which rock do you live under??? Someone with a general thyroid condition “may” experience some improvements with a “simple pill” but not for someone with Hashimoto’s Thyroiditis (Hyper or Hyper) For the MAJORITY it comes down to 90% diet and 10% doctor that can understand that your thyroid controls almost every action in your body and ABSOLUTELY EVERYTHING is affected whether its Zinc, Iron, Iodine, Vit B blah blah, blah, the list is bloody endles…..but I am not going to bore you with that, Mark has written and referenced enough articles and champions for you to educate yourself better before making your next incorrect generalised statement. PS Fruits and Vegetables are most certainly allowed, not just all of them but enough to get by on a well balanced varied diet.

        1. I do have Hashimoto’s, and Levothyroxin did the job perfectly for me for years. In fact, it probably still would, but I use Armor now instead, since with approaching menopause some symptoms crept back slightly, and it took care of them. I know there are a few who have trouble finding the right protocol, but saying Hashimoto’s is a particularly difficult condition to manage simply isn’t true – it’s about the easiest endocrine disorder there is, medically. (Do you perhaps mean Grave’s Disease? That is indeed trickier.) If your doctor has had that much trouble helping you, have you gone to an actual specialist? Endocrinologists are MUCH better at this than general practitioners, typically.

          1. You are certainly entitled to your opinion but many will disagree with you about Hashimoto’s being easy to treat. Synthroid failed me miserably and I begin to improve after finally adding T3 and more so after switching to ZC. And yeah, I’m being seen by a very good Endocrinologist. I don’t expect you to follow suit and vise versa.

          2. Anna, I have no idea of why you would join a site dedicated to the health of people using diet and exercise. I think you need to join a drug company sponsored site, or perhaps you are paid to be disruptive.

          3. I’m sorry, but that’s absurd! I have found the primal diet and lifestyle very helpful and healthy on the whole. That does NOT mean that I’m bound to accept every “alternative” health claim out there as gospel! Especially in an area like Hashimoto’s, where the modern treatment is, in fact, remarkably effective and well-targeted (at least compared to what it modern medicine can offer for most diseases), and where there’s little to no evidence of benefit, especially for recommendations as extreme as the one above to eat absolutely nothing but meat! (In fact, as I believe I have read on this very site recently, hypothyroidism is itself a reason for some caution even in going low-carb.) Is your idea that no-one can honestly be interested in what Mark has to say unless they’ve turned their brains off? Because that sounds like what you’re saying!

      2. Would it be worth it for a diabetic to cut carbs? People take Hashimoto too lightly. You obviously don’t have it; if you did you woldn’t reduce it to the taking of one pill a day and be done. 1. You are constantly on a roller coaster as it’s not so easy to keep a hormonal balance. 2. It has many side effects; like bone and teeth health and cholesterol ratios to name a few. What you are basically saying is, lets medicate ourselves and eat whatever we want – no thank you. Take yourself back to the 1st time you heard about staying away from grains and vegetable oils and increasing your fat intake. Did it settle with you right away, or did you continue to 2nd guess and search on line for a while? Same thing here. There’s this notion that vegetables are innocent but as it turns out, along with whatever vitamins they pack, they are also loaded with anti nutrients and poisons that are meant to deter others from eating them. If one can handle them without ill effect fine, but why eat them when you knowingly know that they are bad for you? Besides, meat along with connective tissues (bone soup) has everything we need.

        1. As I said, I do in fact have Hashimotos. I don’t experience a roller coaster at all, nor should most people – the body converts T4 to T3 at a basically steady rate, which is why Synthroid is one of the least problematic medicines out there. If I had to have a chronic illness, I’m immensely grateful it happened to be one modern medicine actually has a decent fix for.

          As to “eat whatever we want” etc., I’m not saying that. But from all I’ve seen, there simply is no good evidence out there about diet and Hashimotos and I’m not about to stop eating fruits and vegetables on hearsay and anecdotes – in my opinion that’s objectively and clearly harmful, unlike (in my opinion) my Synthroid or Armor.

          1. Anna that’s quite a hefty statement that you said the body converts T3 or T4 to T3 by taking the synthetic Levothyroxine it would depend on your DNA some people do not convert on a cellular level that is not an absolute so thank God there is a natural desecrated as your thyroid is in your body it makes T1 T2 T3 T4 and calcitonin some people are lucky enough that their body cellularly can recognize is synthetic T4 but there are many many people that is not the case do too many other epigenetic factors

          2. Yes, I realize that some people have trouble converting T4 to T3 (although that problem is not particularly characteristic of Hashimoto’s so much as other thyroid problems, as far as I understand). But my point was about the alleged “roller coaster” effect. If your body can’t utilize synthetic T4, that’s unfortunate, but by the same token, it shouldn’t then cause a “roller coaster” effect, should it? Logically, it should simply leave you effectively untreated and hypo, no? If someone’s experiencing up-and-down spikes, is that on Synthroid or on a more “natural” T3 supplement they’ve opted to take instead because they fear the synthetic version? My suspicion would be the latter; old-fashioned, more “natural” treatments of hypothyroidism did indeed have this problem, as I understand it.

          3. Anna, I take Synthroid and T3 cynomel (both synthetics) which is the Eurpoean version of cytomel

        2. I too have Hashimotos and don ‘t experience a hormonal roller coaster. I’ve been on the same dosage of levothroid for 15 years. Vegetables and fruits make me feel great. You do what works for you, but p!ease stop making sweeping genera!nations about “all” people with Hashimoto’s.

          1. Margaret, good for you! It’s not like fruited and vegetables gave me cramps etc. It has to do with the inability to reach optimum and stable thyroid levels no matter what over many years; and trust me when I say that the Dr’s I have excess to, don’t rely on TSH test and be done but run the whole panel. It’s amazing how personal you and Anna are taking this. Why is so important to you? It’s as if you are trying to stop something from happening and don’t tell me it’s because you “care”. If someone wants to try ZC AIP diet, it’s his/her prerogative to investigate other venues and make other aware that it has its place. You want to be on thyroid medication for the rest of your life? That’s your choice

      3. For what reason would you limit fruits and vegetables for Hashimoto’s? I can see eliminating or limiting goitrogens, but why else would you remove every other vegetable?

        1. For one, they are over rated. When the gut – blood barrier is compromised you want to take out everything that has an impact, so that it can heal. Once you’ve done that, you can consider adding back certain item.

        2. Even eliminating goitrogens is based on the sketchiest evidence; from the actual evidence I’ve seen it’s only indicated in the presence of iodine deficiency – not a problem for most of us in modern societies.

    4. Whoa! Misconception alert. I have Hashimotos and followed the AIP diet for a solid 9 months. This diet is all about vegetables! Lots of vegetables, minus nightshades. Fruit is also allowed, however, my functional medicine doctor recommended limited fruit (blood sugar issues) and stressed eating berries over other fruits for their antioxidants. It took a lot of effort but was so worth it. I followed a nutritional supplement protocol aimed at gut healing and sealing as well, so I don’t know how much was the diet or the supplements, I’m guessing it was both. I’m back to enjoying eggs, dairy, coffee, chocolate, etc….without the dietary distress I had experienced on a daily basis before. Two thumbs up for AIP!

      1. Alison, are u still taking medicine? Just because a practitioner say it’s OK doesn’t meant that it is. All stone fruits are out. And did you know that blueberries also not recommended? It’s one thing to fell better and another to go into remission and that is my intended goal. While I felt better on primal and more on Keto, I feel even better now. Recent blood test are good and A1c improved from 4.6 to 4.3. It’s normal for people to react this way to ZC. Is it any different than the reaction to going primal or keto? NO

  3. Seems very similar to a lectin free diet that Dr. Gundry has written about, although his diet allows pastured eggs, coffee and dark chocolate. Mark, as paleo eaters, we generally avoid things that are high in lectins(grains, legumes, etc) but in his book the Plant Paradox, he also warns about too much protein in our diets. He also warns about cancer risk of red meats, even pastured meats, due to some antibodies present in red meat. Thoughts?

  4. I am a huge fan of Primal. It totally changed my life over 3 years ago. But sometimes, even Primal isn’t enough. I have been on AIP for several months after discovering two years of unknown toxic mold exposure. I figured out (via elimination and reintroduction) that grass-fed yogurt was causing me a very inflammatory reaction by this point (it’s likely the mold induced new food sensitivities). I discovered that I was reacting to mycotoxins in many nightshade spices like black pepper and paprika, which left me wiped out after every meal. I went AIP as a precautionary measure to prevent further damage to my gut (mold and mycotoxins are already potent gut damagers) and prevent developing actual AI, especially since my markers showed a risk of developing Hashimoto’s thyroiditis.

    I would like to expand upon the statement, “Most people don’t have an autoimmune disease and don’t need to go on an autoimmune protocol.”

    AI disease is surprisingly common, often going undiagnosed. But more importantly, the modern world poses many threats (especially environmental toxins) that leave people (especially with genetic predisposition) vulnerable to AI. Sadly, many of these toxins are invisible and cannot always be controlled. It could be the glyphosate on your conventional vegetables, the chemicals in your shampoo and makeup, the hidden toxic mold growing in your home.

    It happened to me. I went from 18 years old, eating a perfect Primal diet, and 8-pack ripped to 20 years old with erectile dysfunction and fatigue so overwhelming biking 1.5 miles was exhausting, and on the verge of autoimmune thyroid disease. Chronic illness is very real and is not something to be taken lightly or dismissed as irrelevant to you. I used to be that way, until it happened to me.

      1. They’re not! They grow as pepper corns on pepper trees, not herbaceous plants like nightshades such as bell peppers and tomatoes. But if something has the same name, an alternative health blog somewhere will tell you it’s the same thing!

        1. The piperine in black pepper makes it easier for your body to absorb both nutrients and antinutrients.

    1. You have classic symptoms of a severe B12 deficiency. Often the blood test won’t show it (it shows inactive B12 as well as active, so you’ll have to look deeper). It might be an autoimmune-induced, like Pernicious Anemia. I happen to be a Mark’s Daily Apple reader, and I’ve also dedicated a good part of my life to help people with B12 deficiencies and Pernicious Anemia. You might wish to check that out:

      Good luck, hope you sort it out.

  5. “No chocolate either.”

    Mark has finally lost his mind. 😉

  6. I tried the AIP for psoriasis. It didn’t result in much improvement, so I only lasted it out a few months. I decided the stress involved in following the diet and not having a social life wasn’t worth the small improvement in health. But upon reintroducing foods, I learned that nightshades are a big trigger for me, so that’s something.

    1. My son, my brother and I, our psoriasis improved tremendously when we stopped eating gluten. My son started eating a little bread again and it flared back up. Lesson learned.

    2. I have psoriasis too and tried the AIP. It was hard and it took time, but the symptoms dissapeared after 6 months. I also started to suplement Vitamin D. Afterwards I introduced all the foods again, one by one, with success. Except one: A1 dairy, absolutly ok with goat, sheep or A2-cow dairy.
      Now I’m perfect and happy, no symptoms at all and eating all (paleo fiendly) foods except A1 dairy. And my skin is smoother and brighter than before.
      AIP is really hard but it deserves a try if you suffer an autoimmune disease.

      1. That’s really interesting! I didn’t know about different types of casein. I wish I could give A2 dairy a try.

      2. How soon did you start noticing some improvement? I tried AIP for one and a half months, it was just too restrictive for me, but during that time I so no improvement at all, so it was pretty discouraging. I couldn’t tell if it was helping at all or making it worse… Since sometimes I’d start getting some weird joint aches I’d never had before.

        1. It took a while until I noticed some improvements, around two or three months.
          You have to be really strict with the protocol, but watch also sun exposure (or VitaminD supplementation), stress management and sleep quality. You never know which one of them is affecting you more, or even a combination of all. Good luck.

  7. Is there no reason for concern here that such extreme diet restriction in the absence of much evidence at all (or rather any evidence, for all but the two conditions in the single study you point to), could actually cause harm?

    E.g., we now know that the well-meaning but unproven advice pediatricians dished out for years about avoiding various foods in pregnancy and infancy actually caused many, MANY more children to develop those allergies than would have, if that advice had never been given. Is there no analogous danger here? What if people actually teach their bodies to treat certain foods as poisonous through unnecessary avoidance?

    1. From the article:
      “If you’re the type to obsess over food, and you know your sensitivity is a psychological hang-up rather than a true autoimmune response, skip the protocol”
      touches on the problem, but ignores the aspect that if you do have an autoimmune problem, you are more than likely to start obsessing over foods (if you dont already) and start projecting all sorts of ideas onto the situation. This is clearly going to affect the situation. Mark focuses on the mechanical aspect of foods: I value this, but feel it’s just one side of the coin. The other being how connected / grounded we are, how much crap we have in our minds – stress of any kind, including e.g. ‘I *must* eat this’; ‘I must *not* eat that’; ‘if I eat that I am poisoning myself’, etc. etc.
      FWIW I have had a relatively minor autoimmune problem for years now (alopecia) which got dramatically worse two years ago when I was under a lot of stress. It’s pretty clear to me, for me – I may have to change my diet – but I also need to change the ways of thinking that allowed me to get so stressed up.

    2. I don’t have studies, just an anecdotal recommendation. My AIP protocol gave me back the abiliry to eat the food that I could no longer eat. What really pushed me was research that shows removing gluten is not enough for most people and that the body starts to treat other foods as If they were gluten.

      So I did GAPS for two years and can now eat small amounts of all of my pain foods without pain (except for wheat. Even shampoo with wheat gives me problems). For example, I still can’t eat falafel and hummus(too much legume in one meal) but I can now chose one (usually falafel) and not fear having two days of bloating,pain and gastrointestinal distress…

  8. I did 5 weeks of strict meats-and-greens, which is more restrictive than the autoimmune.

    It cleared my skin completely. But I pretty much went insane by the end of it, so I eat fruit once a week and accept the zits.

    Fermented dairy & nuts made no difference for me, but I avoid yogurt 6/7 days/week just in case.

    PB is a trigger for mild eczemas.

    Weight loss did not result.

    So, now I know. I think experimenting is fine, as long as you do not keep the unnecessary restrictions in place.

    1. @Domi couple of questions:
      why would fruit cause you zits? (Were you eating it after meals?)
      What’s ‘PB’?

  9. Excellent article and one I’ll be sharing with my coaching clients, for sure!

    There are tons of great resources on AIP out there…but SO much information that it can easily cause overwhelm (all the more so when someone’s suffering and trying to find a solution). This post is so simple, clear and immediately useful.

    Also love how it outlines when AIP can be helpful and powerfully healing…and when it’s not optimal. Thanks, Mark!

  10. I have celiac, which is an autoimmune disease, but easily controlled by not eating gluten. Is there value in trying the AIP for me, as opposed to say, someone who has MS and is dealing with symptoms? I’m curious if I could feel even better, but generally I don’t think celiac affects my day-to-day life.

  11. I am what you could call an AI nightmare. I have RA, sjogrens, psoriasis and celiac. I suspect I’ve had celiac since I was a child. I went AIP for almost four months. I improved a lot but continued to have the hallmark symptom of stiffness in the mornings related to RA. i could not put shoes on for an hour! As a matter of practice,I would go AIP for a month a quarter as a reset. Terry Wahls has different ideas on AIP. I tried her lower carb version but found it very hard. When Sisson came out with Keto Reset I gave it a go. (i am a certified PHC). To my surprise, two weeks into it ,I had no stiffness.ZERO!!! I have gone back to 30-100 carbs per day intermittently and have had no return of my stiffness. I have been able to go four weeks between Humira instead of two. I ate dairy, eggs and night shades. I never felt stressed out about food, never felt hungry , and enjoyed my time going keto. Personally, I can’t say it would have worked had I not been previously on AIP. I do know that food rotation helps me a great deal. Eating ANYTHING on too regular a schedule seems to impact me. I eat dairy intermittently’ red meat,fish,poultry etc. I vary my greens and other veggies as much as possible.Don’t give up! You never know what will bring you relief. I agree with Mark 110% about obsessing about food, that is more detrimental to a person than anything. Good luck to all of you dealing wit AI disease. May you find what works for you.

  12. Thanks Mark, like you say sometimes there is more to it than just eating AIP, my husband has been eating AIP for over a year for his RA which has helped immensely but the presence of klebsiella is making it a long process to heal his gut and he is reluctant to introduce many foods until that has cleared. So for anyone who has found that AIP doesn’t work so well for them they may want to do a bit of further testing.

  13. Vinegar isn’t necessarily a good choice since it’s high in histamines, which some people don’t tolerate well. Lemon or lime juice is usually a good substitute for vinegar. Bone broth can be high in histamines as well.

  14. I’m curious how the AIP protocol helps those with an autoimmune disease in which the damage is already done. I have Addison’s disease (primary adrenal insufficiency). My adrenals have already been damaged – there is no chance of them working again, so would something like an AIP actually be of any benefit? Honestly, I think the stress of following such a strict diet would make me sicker than just eating a normal, variety filled primal diet.

    My same thoughts apply to Hashimotos – I’ve had it for years, I no longer have increased antibodies, at this point my thyroid is toast – is such a restrictive diet really going to do anything?

  15. A long time ago I would have laughed at this. I had asthma since a baby… always had an inhaler, steroid, hospital stays, oxygen tents, emergency shots to open my airway (twice I almost died). I removed milk on a vegan diet in my 30s. 8 months in hubby said, Hey, You have not had an attack in how long? BINGO… I did not stay vegan but I never added milk back into my diet and now the world opens my eyes to all the allergies that I never knew I had. BTW- I LOVE the Paleo Diet!

  16. I have very early stages MS and was lucky to catch it when i did, I use the auto immune protocol to very good effect, thought I fail to stay on it all the time. By basing most of my meals on meat, veg and herbs I keep it simple. Coffee is a big issue for me, I love the stuff but there is definitely an inflammatory response. If I can keep my coffee intake down to two or three a week I am good, but daily is too much.

  17. I need the AIP to have serious respect from the paleo/primal community. I consider myself paleo, but need to avoid coffee, chocolate, PB, spices, alcohol and most fruit. It’s a dreadful pain, especially when I read about all of you enjoying your morning coffee, and afternoon chocolate, or glass of wine on the weekend. Maybe other foods are a problem too, but I can’t seem to get myself to avoid eggs, nuts or nightshades for very long. I have IBS/D, hypothyroidism (but perhaps not Hashimotos), RLS. Even if these are not AI diseases these foods are still triggers. Been eating paleo for 11 months now and have healed considerably with fewer and less serious flareups. I fully expect that different diseases will have different triggers, for eg, gut issues should probably be low carb to help restore bacterial balance. Full ackowledgement that other lifestyle factors are equally important as Mark mentions. It’s not that one program fits all, but that these communities are educational, helpful, supportive and open to all who seek better health. Thanks everyone!

  18. I didn’t do AIP, but I followed GAPS for two years. When I went primal (and stopped being a vegetarian of fourteen years) at age 28 I felt on top of the world. I realized the horrible stomach pain I had put up with most of my life was related to gluten. After remove grains, soy (and wheat!), my energy, health and outlook on life was fantastic. Then when I turned 30 I lost my job and gained 45 pounds in 6 months. I was depressed and at a loss for my life purpose. I began going to community college and the work helped give me something to focus on.

    At the same time digestive symptoms that were similar (but not on the same pain level) to my wheat and gluten issues arose. Almost every meal (primal or not) gave me distress. So I gave GAPS a try. I found that raw vegetables (especially carrots) did not digest, nor did I find dairy, legumes, nuts and really starchy cooked vegetables be digestible. GAPS also gave me the courage to add a lot of fat to my diet (along with collagen and bone broth, all three can be very healing to the gut). GAPS didn’t cure my ails, but after the protocol I can eat all of the above food in small qualities without fear (except for wheat).
    But, I didn’t truly regain my health until I began to do short fasts. So far I fasted two, three day fasts, one five day fast and one six day fast. All since last July. I still have about 15 pounds to lose, but I don’t result caste any more because I have my health and energy back. I don’t get sick when the whole campus does, or if I do I go to bed an hour early and by the next morning I am over it. I think an AIP protocol works even better when combined with fasting

  19. There is a webinar going on right now about oral health and health problems caused by root canals and amalgam fillings. If people have an autoimmune disease, they should get checked by a holistic dentist for these things first.

  20. Went on Dr Grundy’s diet which is very simular. My ashma (autoimmune disease) which I have had for over 40 years diapeared in three weeks on the diet. I am not sure what did the trick but I will stick to it. Using inhalers was no fun and they do not know the long term effects of using inhaled steriods. I am sure my triathlon times will improve especialy after reading your book Pimal Endurance.

  21. The ultimate autoimmune protocol diet is simply meat (including seafood) and water which ironically is what our ancestors primarily ate before the age of agriculture.

    1. I find that hard to understand, so many people are allergic to seafood. Or is an allergy that much different from an intolerance?

  22. Yes I tried it and I didn’t complete it, I got sicker than I ever was and ever been since. I’ve lost 15 lbs in 2 weeks, plethora of new symptoms, it was not fun. Not to scare anyone off, it may have been completely unrelated to my new diet.

    I’m totally sun deprived right now, good thing it’s spring soon! (also maybe a little bit nature deprived too, does snow count as nature?)

  23. Has anyone had any luck with the AIP and ankylosing Spondylitis? Primal/Paleo helped a lot and got me off my NSAID’s but not 100% better. Wan’t to try the AIP but I’m so busy with 3 kids and work that its hard getting my head into it.

    1. Hi Andrew. To my knowledge most improvements can be made by following a low/no starch approach. Search for Charles Comey at PhoenixHelix dot com.

      Hope that help you in the right direction.

  24. Hi Mark! I got diagnosed with an AI condition last year which my doctor suspects I’ve had all my life. The good news is, because I’ve been suffering from so many symptoms, I got turned on to Paleo 7 years ago, so switching to AIP, which I did in November, hasn’t been mindblowingly difficult. It has changed my life though! I feel better, have a normal amount of energy, a normal metabolism, etc when I stick to it. It IS a challenge. Every. Day.

  25. Interesting how reverting back to the basics of eating can improve your health. We are pursuing a keto diet primarily for maintaining my husband’s and my weight, but also to treat his arthritic pain issues and my leaky gut issues. This may become an interesting next step, but for now; getting used to the Keto Plan will suffice.

  26. “Nightshade vegetables, such as eggplant, potatoes, tomatoes, peppers and okra.” Okra isn’t in the nightshade (Solanaceae) family, it’s in the Malvaceae family.

    “Wait. Damnit. Chocolate is a legume, and legumes are out. No chocolate either.”
    The cacao tree is also in the Malvaceae family.

      1. I’m currently trying an AIP protocol WITH ONLY Low FODMAP fruits and veggies. But basically only grapes as most fruit bothers my stomach. Basically my food list fits on an index card.

  27. I tried the AIP diet for 4 months a couple of years ago. I hated the diet. Before that I had been living Primally for 3 years.

    I was diagnosed with SLE in 2001. Doing the AIP did nothing to get me off my meds for Lupus, and at the time I was involved with a couple of AIP discussion groups. Not one person who had SLE reported any significant changes from those groups. A lot of the people in the AIP groups suggested eating AIP for years, if not forever. That it takes years to see results. I don’t believe that. I think our bodies are more resilient than that and will respond much quicker.

    I love living primal but still have issues with regular inflammation throughout my body. I’m considering trying AIP again after reading Mark’s article. I think it will be easier this time around. It will not be hard for me to eliminate everything immediately as I have been very comfortable with eating ONLY Primal foods for more than a year.

    I’m just not sure that SLE will respond to the AIP, as before. Anyone have any experience with this?

  28. I have Celiac Disease and self-diagnosed over 15 years ago, but then even though our house was 100% Gluten FREE my gut symptoms returned… Found out it was SIBO. I’ve been on this extreme diet (start with only a bone broth fast for the first 2 weeks and don’t add in a new food [listed in 5 stages in the Specific Carbohydrate Diet to be added in that order] only one per week.) It’s been a year and I’m happy living with my extremely limited diet since ALL my symptoms are gone and I’ve got more energy (and 25 less pounds) to do even more athletically than ever! This is too extreme for most, but for those who’ve suffered leaky gut, autoimmune symptoms, etc. it’s a life saver!! I knew I’d never tolerate gluten or dairy, but found my allergies to nightshade, beans/legumes and PROBLEMS with SUGAR. Hooray for honey in small amounts and yes, I can tolerate small amounts of coffee!

  29. I’m thinking of trying it, I’ve noticed that vegitables if they are uncooked are a problem, they don’t start to digest it seems until they “cook” inside me. Then I notice that even cooked ones seems to take “the express” out, ew! So I’m eating them every so often and concentrating on good sources of protein and fat for now. We’ll see if after a while I can add some in here and there more often. Salad is a HUGE problem, sadly!

  30. If I had some serious issues I was dealing with I would definitely give this a try. But just going Primal/Paleo changed my life after 30+ years as a vegetarian. For me coffee would be really hard to give up…it’s truly a pleasure for me. And eggs. Don’t eat them every day, but would be tough to completely eliminate.

  31. I tried the AIP in 2016 for 4 months trying to reduce inflammation from SLE. I was diagnosed with SLE in 2001. AIP didn’t do much to help my symptoms and I never got off my meds.

    I was a part of a couple of AIP forums at the time and not one person who had SLE reported any benefits. Some said that it would take YEARS on AIP to see results. Since I hated the diet, I was not willing to do it that long. After four months I went back to Primal (which I LOVE).

    After reading Mark’s blog I am considering trying again since I still have regular inflammation throughout my body.

    Anyone have any experience or ideas about this?

  32. Does anyone have experience with ulcerative colitis? I’ve had it for 20 years, treated with meds. For the last 10 months, I’ve changed my diet to be mostly plant based. Am now off the meds, but recently starting getting decent gas in the afternoons and night. Thinking about AIP…

  33. I thought my diet was good before AIP and thought AIP wouldn’t help much. But how wrong I was. I am glad I gave it a chance. I am an AIP believer. AIP diet cut my inflammation and helped cut out my migraines in addition to helped with blood sugar management (I am at Type 1 diabetic), reduced my aches, pains, and stiffness. I have faster body ache recovery. And I cutting my insulin use by 1/2. I have reintroduced nuts and seeds, stevia, and occasional eggs, beans, dairy and nightshades. But because I had amazing results, I am eating much less of these foods. I never eat grains of any type.

  34. I did 2 months strict AIP but didn’t reintroduce systematically so still don’t know what the worst offenders are for me apart from nightshades. (I have fairly mild autoimmune issues, skin and thyroid) However it was fascinating. After one month I stopped snoring and my whole body lost it’s middle aged stiffness, my mind was clear with no brain fog. I slept so well, waking up totally refreshed. I’d love to try again, this article might just be the prompt I need, but you seriously need to plan your shopping ALL THE TIME. And people think you are completely bonkers so you need to be warned about that!

  35. Chocolate isn’t a legume, as a couple of people have pointed ou, so hopefully Mark will address that. I don’t eat commercial chocolate, but make my own with raw cocoa powder stirred into melted coconut oil and/or cocoa butter. No sweetener, but it doesn’t half taste of chocolate!

  36. Yes…. it can work!!!

    Hi! I was diagnosed with Ulcerative Colitis since 1998. After years of mis-diagnosis, uneducated doctors, my own research, and reaching out to bloggers, I stumbled across Phoenix Helix and the AIP. I started with her book, A Simple Guide to the Paleo Autoimmune Protocol; which was much easier to digest than other books on the market. It took me a year, almost exactly to finally bite the bullet and start the AIP. This was the first of September 2017. Yay! Finally! I started re-introductions sometime mid-October. It is very interesting to me to notice and finally find out how foods affect me. I was so done with either being afraid to eat something or not knowing what made me feel so yucky afterwards.

    My Ulcerative Colitis has not been this good since 1998 –seriously. Don’t try this at home kids, but I also stopped my Lialda about mid-way through the elimination faze and I haven’t looked back. I am astounded at how much better I feel and look. The bleeding stopped, my joints were not painfully achy while I was at rest, I could finally sit still without having to move in order to alleviate pain.

    I had a minor set back Thanksgiving week because I ate some fresh shrimp that were supposed to be boiled with lemon juice only. I found out the Zattarain’s boil bags had been used which contained lots of nightshades and seed spices. It has taken me a week to get over that and since there were so many “restricted” items included, I don’t know what affected me. My joints hurt really strangely among other things. Thus the perils of eating something I didn’t prepare myself; and boy did I pay for that. Proving how important it is to stick to the AIP and not slip up.

    We had to go to a relative’s wedding about 30 days in and took our own food –which worked out quite well. 🙂

    Preparing every single meal for two, three times a day, since September 1st has been quite the adventure. It is not that it is difficult for me to plan and be prepared, it just takes soooo frickin long to cut, prepare, and cook!!! But…. not feeling sick or having allergies almost constantly has been beyond rewarding. Not having to worry I won’t make it to the bathroom at any given moment is beyond what most can comprehend. 🙂

    My most interesting n=1 experiment:
    Though citrus isn’t considered something to be eliminated, I already knew I had allergies to citrus so I had eliminated lemon because I just wanted to know. That being said… I first tried some lemon juice in my turmeric “tea” that I often make for myself. (Turmeric, water, collagen powder, coconut oil, raw honey) Within 20 minutes and for the following 3 hours, I felt like I literally had the flu. I felt SOOO sick! It was weird! I waited until I felt better and tried the same again –with the same results. That got me thinking to last winter when I seemed to have the worst feeling flu I’d ever had that seemed to make me feel horribly sick longer than usual. I assume you can guess what I was constantly drinking for congestion and sore throat…. warm lemon and honey water. Geez…. that’s probably why I felt so sick for so long! I haven’t tried other citrus foods yet.

    I’ve also had reactions to canned tuna. I kept blaming the spinach. If you’re curious, search HIT (histamine).

    Did you know that eggs can be evil? So can dairy and garlic…. Prior to beginning the AIP, I had just found some delicious frittata recipies and one of my new favorites was adding an over-easy egg to a bacon, carrot, and spinach salad. Eggs (both the white and yolk) caused digestive issues. I will someday try some of these things again, but for now, LOL C’est la vie I guess.

    While this is still a work in progress, and unfortunately but fortunately for me, myself, and I….. this will be a lifelong pursuit as know for sure that I am eating to live, not living to eat.

  37. I have been a long time follower of this blog but missed this post for some reason and just happened upon it today so thought I would advise of my experience with AIP even though this topic is months old.
    I am a 38 year old female who was diagnosed 10 months ago with an aggressive form of vasculitis called Wegener’s Granulomatosis. I had suffered with a number of symptoms for years and never understood that all of my symptoms were being driven by the same underlying cause. Last year that came to a head when my symptoms escalated and the disease began necrotizing the blood vessels in my face. I have permanent disfigurement with the cartilage in my nose and pieces of my ocular bone now missing as well as significant recession of my gum tissue. Luckily a diagnosis was finally discovered before the disease could spread to my lungs and kidneys and I have since been on a course of high dose prednisone and methotrexate (the chemotherapy agent).
    A friend of my sister had suffered from ulcerative colitis and had been introduced to AIP and she recommended I look into it upon receiving my diagnosis. I would say the benefits for me have been two fold.
    1. I have managed to keep my prednisone related weight gain to just 6 lbs in 10 months due to the relatively low carb nature of the diet. I maintained some degree of exercise throughout the last 10 months to preserve as much muscle mass as I could from the catabolic effects of the steroids so diet AND exercise were important but I consider it a major contributor nonetheless. While certain starches and fructose are allowed I was cognizant of limiting the insulin reactivity exacerbated by the glucocorticosteroids and I feel that I was able to manage that much better while still optimally feeding my body for recovery. Nutrient density is a primary focus of the protocol so contrary to some of the comments responding to this post,, vegetables are a big component of the diet as are organ meats, organic grass fed meat and wild seafood.
    2. The second benefit has been a drastic calming of my overall nervous system though it took a good 6 months of strict adherence to really observe those symptoms which manifest in better moods and lower anxiety and very low inflammation markers, and which have enabled me to begin tapering my medication. My doctor has been extremely concerned about remission through the tapering process but I am confident that AIP and other lifestyle changes are actively assisting in keeping the disease at bay. Due to the doseage of prednisone I have not begun food reintroductions yet (as I didn’t want the effects of the medication masking inflammatory responses to certain foods), but I am hoping to begin reintroductions by year end. As critical as medication has been for me to get the disease under control, I believe without the diet I would still be extremely sick. I would (and have) recommended this to numerous people asking my advice around treatment. As life altering as it has been I cannot sing its praises enough. Without it, I believe I would be dealing with a very uncertain future.

  38. I just finished a vegetable/juice detox of 5 days and now I’m slowly re-introducing fish and vegetables. I have a family history of rheumatoid arthritis an just experienced my first flare up after a very busy summer prepping for a body bodybuilding show, eating tons of coffee and wheat. I am following the anti-inflammation diet as outlined here and in Sarah’s book. I’m looking forward to the results!

  39. I just completed 31 days of strict AIP for Hashimoto’s. Funny thing is, I think it triggered a flare because of the emotional and relational stress it caused for me. I obsessed about being compliant, felt isolated and deprived, and spent entire weekends shopping for and cooking the meals. I didn’t even feel bad prior to beginning AIP, but wanted to see if my antibodies would go down (stay tuned). I will be introducing some foods, probably not in the “correct” order, but foods I never had an issue with in the past and foods that make it easier to have a night out with my husband or friends. I believe this protocol has its place for many, I’m just not sure it was right for me.

  40. I have really enjoyed reading this article especially the witty bit…! beginning any elimination diet can feel overwhelming. Good luck to anyone starting this . Stay strong!