AIP for Autoimmunity: Is it ALWAYS the Answer?

[This post is adapted from the chapter, “Why This is Not Another Paleo or AIP Cookbook” in my #1 best selling Essential Thyroid Cookbook.]

If you’ve been tuned into the online communities related to thyroid health, Hashimoto’s, and other autoimmunity, and perhaps read many of the same books and blogs that I have, you’ve likely heard of – and likely tried – a Paleo (aka ancestral) or AIP (autoimmune protocol) diet. These diets help to heal the intestinal lining, which is critical for those with any manifestation of autoimmunity.

My position on Paleo/AIP:

  1. I see merit in the Paleo and AIP diets right out the chute – in some circumstances. I explain below.
  2. I’m wholeheartedly skeptical of removing whole food groups from the diet, even for people with autoimmunity.

There are varying twists to these diets, but generally, with a Paleo diet, you’re eating what is believed to be the foods that our ancient ancestors ate, as in, what they foraged for: meat (grass-based/pastured), fish, vegetables, fruits, nuts, seeds, herbs, spices, eggs, unrefined coconut and olive oil, and animal fats like ghee (butter oil), lard, and tallow. According to some Paleo proponents, fruits are off limits – others only support eating berries.

Foods not allowed include grains (including corn) and legumes (including soy), dairy (although some allow grassfed dairy), sugar, caffeine, and oils derived from seeds and grains, which can be high in inflammation-promoting Omega-6 fatty acids. Some claim no eggs and others say no starchy vegetables because they can’t be eaten raw.

[You can read my 2012 post questioning the merits of Paleo – especially for those with hypothyroidism – here.]

An AIP diet, for those with autoimmune conditions, is similar to Paleo, but in addition to the above exclusions, eschews nuts, seeds, eggs, dairy, nightshade vegetables, and generally, fruit.

My non-adoption of an AIP diet for both myself as well as my most of my clients and my allowance of non-gluten grains, legumes, nuts, and seeds is thoughtful and intentional, based on years of personal and professional experience.

I do have some “restrictions” around grains and legumes, which have remained unchanged, even going back to my pre-Hashimoto’s days (both prior to my diagnosis and in my coaching practice):

  1. Largely limit (or eliminate) flour-based products and eat true whole (intact) non-gluten grains, in moderation, because it’s true that a diet heavy in grains can be inflammatory and lead to weight gain and blood sugar dysregulation.
  2. Legumes are a great source of plant-based protein, but I recommend not making legumes the sole protein of any meal, unless you can truly handle them without digestive distress. Even people who don’t have autoimmune conditions can have a difficult time digesting too many legumes.

My upcoming cookbook contains well-researched chapters called “In Defense of Grains” and “In Defense of Legumes” that, in addition to other findings, highlight the research of Justin Sonnenburg, PhD and Associate Professor of Microbiology and Immunology at Stanford and the author of The Good Gut, co-authored by his wife Erica Sonnenburg, PhD. They’ve been trailblazers in discovering how the fiber in grains and legumes improves the health of our gut microbiome.

Likewise, Dr. Susan Blum, author of The Immune System Recovery Plan, regularly mentions quinoa, amaranth, millet, teff, buckwheat, various types of rice, and also legumes as part of her healing program and uses these foods in several of her recipes.

[Lisa and I recognize there are varying therapeutic diet approaches in the Functional and Integrative Nutrition communities that support thyroid and immune health, so our cookbook features user-friendly icons to help you easily decipher which recipes will fit your individual dietary needs at-a-glance. There’s no one-size-fits-all way to make our recipes work for everyone, so we made every effort to provide sensible adaptations to modify them to fit dietary practices such as Paleo and AIP, whenever possible. In most cases, the adaptation may include simply omitting an ingredient or making a simple ingredient swap to make it compliant.] 

Looking Back
To provide context for why I’ve never been anti-grain or anti-legume, I was diagnosed with Hashimoto’s in early 2008. At that time, popularity of the Paleo diet hadn’t crested. The AIP diet wasn’t yet on the scene.

As I began my research into low thyroid function and autoimmunity/Hashimoto’s, the importance of healing digestive function became abundantly clear, given that 70-80 percent of our immune system is in our digestive tract. I began to put one foot in front of the other, which included sleuthing out the dietary triggers that were antagonizing my digestive lining and contributing to the leaky gut characteristic of autoimmune diseases.

In addition to going gluten-free, among other strategies, I did an Elimination Provocation diet – a version similar to the one I share with my clients today. It’s a temporary diet. It excludes nuts – but not seeds, grains, or legumes, with the exception of peanuts (which are technically legumes) and soy (also a legume).

(Many of the recipes in my upcoming cookbook are either AIP-compliant (not that we intended to make them so) or have adaptations for those on a strict AIP diet.)

At the onset of my journey, given that the research around how the phytic acids and lectins – the “anti-nutrients” – in grains and legumes (and supposedly nuts and seeds) contribute to leaky gut hadn’t been popularized, I didn’t know that I “should” remove these foods from my diet. And within a few months, my Hashimoto’s was managed – without the use of thyroid hormone replacement.

Along with my success in healing my autoimmunity came a significant shift in the thrust of my coaching practice – I began largely focusing on helping others with Hashimoto’s. Remember, by now, it’s fall of 2008 – the volume on Paleo and AIP hadn’t yet been turned up. And over those next couple of years, prior to the popularization of the AIP diet, the vast majority of my clients had the same success that I did – plummeting antibodies and alleviation of their hypothyroid/Hashimoto’s symptoms.

If I’ve learned anything in the decade I’ve been a health and nutrition coach (10 years this week!), it’s that we’re all bio-individually unique. We all respond to foods differently – and have different trigger foods. While eggs may be the perfect food for you, they’re an anti-nutrient for me. For some, simply going gluten-free gets their Hashimoto’s managed. When you consider this, it’s difficult, in my opinion, to rationalize an extreme diet, in all circumstances, for every single person with autoimmunity.

In fact, Laura Schoenfeld, Registered Dietitian and staff nutritionist for Chris Kresser, a long-time Paleo proponent, autoimmunity expert, and author of The Paleo Cure, “A strict Autoimmune Paleo Diet isn’t necessary for many people with an autoimmune disease. In fact, there are few people with autoimmune diseases that would need to strictly and permanently avoid all the foods eliminated from the diet, as not everyone with autoimmunity is intolerant to all of these foods.”

Although our approaches differ somewhat, even Kresser’s book outlines eliminations, followed by reintroductions/provocations, based on a flexible Paleo diet. To be clear, he does recommend the exclusion of grains and legumes for those with autoimmunity.

And flexibility is key. Over half of the clients I’ve worked with have tried the Paleo and/or AIP diet. Here are the most frequent comments:

  1. I could do it for a while, but couldn’t hang on – I hit a wall. It was too restrictive.
  2. I did it for several months and I actually feel worse. And my antibodies have gone up. (I know what to look for in these circumstances.)
  3. I wasn’t given any additional instructions on how to heal my gut beyond the diet and didn’t know how long to stay on it.
  4. I travel for work and this diet is nearly impossible when I’m unable to prepare my own food.

Against the Grain…Wait, NOT Against the Grain
I’ve proceeded to coach my clients in the same protocol I adopted – teaching them what I’ve learned by making myself a science experiment, during which I ate seeds and moderate amounts of non-gluten grains and legumes, with the exception of peanuts and soy. Again, nuts are excluded from the Elimination Provocation diet.

There’s the saying, “If it ain’t broke, don’t fix it.”

In years of this work, I haven’t seen the need to tell the majority of my clients to take on an even more restrictive diet than what’s presented in the Elimination Provocation diet. I wanted to see what would happen without asking people to resort to – simply meat and vegetables. And more meat and vegetables.

I love meat and vegetables. And I would even say that I eat a “Paleo template.” But to rely solely on these foods meal in, meal out, day in, day out can take the pleasure out of one of the most pleasurable acts we humans have – eating.

Stress = Antibodies
Today, it’s prevailing theory that all people who have an autoimmune disease need to adopt an AIP diet, but I’ve continued to go against the grain. I simply don’t believe it’s a one-size-fits-all approach and I guess you could call me a holdout – I’m still not convinced that it’s required for each and every person with autoimmunity when, for most people, adopting that strict of a diet can be stressful. It can get old pretty quickly. I know, because I’ve heard it for years from clients – that an AIP diet can became burdensome and unenjoyable.

Some can thrive on the AIP diet and I’m not here to disregard its merits – that’s not my point. But often, a super restrictive diet of any kind is a two-steps-forward-two-steps-back situation. The stress that ensues – at least for some people – isn’t conductive to the healing that needs to take place.

If there’s another way, I’d like to present it, especially when:

  1. There’s enough evidence showing that stress increases antibodies. It’s even said to be a trigger for the onset of autoimmune diseases. According to Dr. Mark Hyman, “Stress worsens the autoimmune response.”
  2. AIP can require a lot of willpower to adhere to long term. Willpower is a finite resource – we have to be careful about how we expend our precious energy.

Many of my clients exhale audibly when I tell them that my approach includes grains, legumes (with the exception of peanuts and soy), and seeds. This said, some have been clear that grains and/or legumes give them digestive distress. In these cases, I’m of course not going to tell them that they’re fine to consume, but that after their gut-healing protocol, they can likely return to eating these foods (and the other foods they’re currently sensitive to), to which I often hear, “Wow, really?”

While some may be directly affected by grains and legumes, others can get their autoimmunity managed while continuing to eat small amounts of these foods – as long as other dietary triggers are investigated. In most cases, it doesn’t take months and years to tackle autoimmunity to the ground.

In a healthy human, the intestinal epithelium regenerates every four to five days – one of the fastest rates of reproduction of any tissue in the body. Given the right tools for healing, it’s stunning what can happen in a matter of a few days and weeks – not months and years.

But it isn’t simply about diet and restriction of certain foods for a period of time. With immune modulation, there are other factors to consider, including:

  1. Addressing toxic body burden, including but not limited to toxins in skincare and cosmetics, food and water, home cleaning products, and exposure to endocrine/immune disruptors such as bisphenol-A (BPA), PCB, and heavy metals. The myriad ways in which we become exposed to environmental toxins is well beyond the scope of this post.
  2. Supplementation that’s been shown to “heal and seal” the intestinal lining.
  3. Possible bacterial infections such as small intestine bacterial overgrowth (SIBO) or Helicobacter pylori (H. pylori).

At the beginning of this post, I said that I see some merit in an AIP diet right out of the chute – in some circumstances. In addition to the foods excluded in the Elimination Provocation diet, I recommend the exclusion of grains, legumes, and seeds, in two circumstances:

  1. When the symptoms of autoimmunity are so painful and distressing as to cause life-altering circumstances. A 49-year old client I worked with had psoriatic arthritis. What had been diagnosed 20 years prior as a fungal infection of her toenails was, in fact, autoimmune arthritis. (She went 20 years without a proper diagnosis!) The pain had become so intense that she could hardly walk, needed to ride in a cart at the grocery store, and, after finding the right doctor and diagnosis, found out that she had deformity in her joints. In these cases, I pull out all the stops and suggest an AIP diet.
  2. When an Elimination Provocation diet hasn’t proven successful. For clients who were dedicated to the process and don’t find symptom relief and/or find that their antibodies have been unchanged or have increased, I recommend:

a)     Eliminating grains, legumes, and seeds;

b)     Getting tested for heavy metal toxicity (this is a good idea anyway);

c)     In cases of continued and overt digestive distress, getting tested for a bacterial gut infection, like small intestine bacterial overgrowth (SIBO) or Helicobacter pylori (H. pylori).

Regarding a) above, the exclusion of grains, legumes, and seeds is much easier when the common digestive triggers have already been identified. In other words, once someone has done an Elimination Provocation diet and knows what they can and cannot tolerate, then the foods that they can handle are back on the table. Thus, the elimination of grains, legumes, and seeds isn’t simultaneous to the elimination of several other foods, making the diet – and healing – much more feasible.

This scenario can explain. You do an Elimination Provocation diet and find that of dairy, eggs, citrus, soy, nightshades, shellfish, corn, nuts, and peanuts, only dairy and nightshades prove to a trigger foods for you. (Gluten should be categorically avoided for everyone with Hashimoto’s.)

If you do find that grains, legumes, and seeds need to be avoided, you can remove them while eating eggs, citrus, soy, shellfish, corn, nuts, and peanuts and continuing with your supplemental digestive healing. You can then reintroduce them in a similar fashion to the reintroduction instructions in the Elimination Provocation diet.

As explained, the Paleo and AIP diets differ, but are similar enough that I want to share this quote from nutrition and health expert, Sean Croxton, who said, “Let’s face it, going 100% Paleo isn’t for everyone. Even me. To the average person, despite its benefits, Paleo can seem intimidating, restrictive, and at times kinda annoying, to be honest.” (Yes, and AIP is even more restrictive than Paleo.)

According to Chris Kresser, “The belief that ‘everyone’ will benefit from one particular dietary approach – no matter what it is – ignores the important differences that determine what is optimal for each person. These include variations in genes, gene expression, the microbiome, health status, activity levels, geography (e.g. latitude and climate), and more. When it comes to diet, there is no one-size-fits-all approach.”

According to integrative medicine pioneer, Dr. Andrew Weil, “There’s no harm, and some potential benefit, in trying the Paleo diet, but I believe the diet is too restrictive for most people to stick with long term. I think success is more likely for the majority if they regard it as healthy direction, rather than as a strict set of guidelines from which one can never deviate.”

Dr. John Douillard states, “The so-called Paleo diet of today is high in farm-raised livestock rather than hunted game, suggesting we ate it multiple times a day rather than in moderation. True Paleo diets were much more diverse and seasonal with a dependence on tubers, veggies, and grains, and much less meat than you might think. The veggies were completely different than they were today. Carrots were tiny and bitter, tomatoes were small and toxic, broccoli as we know it did not exist, bananas would be unrecognizable, and blueberries and avocados would be puny with little fruit meat to eat.”

And if you’ll allow me one more quote, in his article, “Stop Worshipping Ancient Systems of Healing and Eating,” Marc David states, “I have watched too many friends, students, and clients get hooked on traditional systems that are old, wise, often brilliant, well thought out – and not always 100% applicable for humans of this day and age. In particular, many people embrace Ayurveda, Macrobiotics, or the concepts of the Paleolithic diet.

“Yes, these approaches bring tremendous insight and practical knowledge that we have long forgotten. I’ve benefited greatly from studying and practicing the principles of these diets. At the same time, the over-reliance on these systems often results in an intense fundamentalism, personal and nutritional isolation, and a waste of time in trying to follow in a precise and unwavering manner – principles that may have worked great eons ago, but don’t necessarily translate fully into our world today.

“Every old and ancient system needs some updating. Macrobiotics is a great example. The principles in this worldview are powerful and far-reaching. The problem is, most people are practice a form of macrobiotics that works fine if you’re from Japan, but not so well let’s say, if you’re a white dude from Mississippi. The challenge is, can you be bold and creative enough to take what truly works from these approaches, and toss out what doesn’t?”

[This post contains affiliate links.]


I cannot tell you how much I love this. 

I had been feeling really ashamed for following a less rigid plan because I was feeling much better. I was believing that if I was a good enough food planner, my Hashimotos would go away. Now I'm realizing I've done such great work with Jill that I regulate myself and I know when I need to take a better look at my nutrition, even though in general, I'm doing so well. Thank you for this. And keep up the good work!

Joy, thank you for mentioning something that I actually meant to address in this post and forgot – guilt and shame. Guilt and shame for not doing things “right” and “perfectly.” Talk about stress! With autoimmunity, the body is already attacking itself and these feelings are a form of self-abuse – just another form of attack on the self.

Wow, guilt and shame...just what I have been studying about! I have been on a strict AIP diet for 3 1/2 months and have lost 38 pounds and cut my BP meds in half (given permission to get off totally but in the process), and BS is in the 130 range down from 270 when I started. But I am always depressed...I feel like I've lost myself and my life and I can't find my way home...I'm even in counseling. I am beginning to realize that shame and guilt keep me in bondage in this way of eating..."What if I fail?"..."What about all the money invested?"..."What happens if I don't measure up...if I want to change something...if I question something?" I think there's a lot to guilt and shame and this way of eating and I don't pretend to fully understand doctor isn't listening to me and keeps my plowing ahead. I just want my life back...and I want to be healthy. Can you not have both? 

You can have both. :)

I think I need a consult with you...I'm very interested in hearing what you have to say! In the meantime, I will read your blogs and see what else I can learn. Maybe there is hope!!

Great post! It's always nice to be reminded that this is an individual journey and we can learn to listen to and trust what our bodies need to heal. I know you have a hard stance on eliminating gluten but I'm curious - can it ever be re-introduced if our antibodies become very low or dissappear?

Jill, As always your perspective honors the complexity of each individual while truly exploring the science and the diversity of opinion on healing the gut and the immune system. Strict paleo is for me like strict macro, just not something my body wants. Elimination and provocation was a revelation. Things I thought were fine, we're not and I am so much healthier from the discoveries.  And fruit is definitely back IN and I'm loving it. Thank you for your continued honesty and complete review of all perspectives. You truly teach and heal in the most comprehensive way. Many thanks! Ana

well written, well researched, and balanced.  Thank you, Jill.

once again....I think you're great!


this makes a lot of sense I've been struggling with aip due to children and lack of funds lately .. And had the mind set all or nothing .. I've always hsd hashimotos as far back as I can remember . After my oldest son was born I had major flares and was in pain over weight and puffed out . I adopted a very healthy diet not really eliminating any food gripe but I had s lot of will power and ate a lot of vegetables meat little rice and pot but I did not eliminate wheat and dairy tho I do remember I naturally ate very little of . I looked felt great I had s lot of stamina . I did have flares after eating rich good like Chinese but it was temporary and I'd quickly go back to healthy food and so id feel odd for s day then good again . after my third son I've felt awful and struggle with food and I felt ok so I had s bite of donut may as well eat three . I did do aip last year for three months snd was great after that doc put me on ndt and I went majorly hToo and I found It difficult to focus felt bad and lost the stamina . Thanks so much for this piced of writing it has given me the ok to go back to my old ways of eating healthy but definitely excluding gluten and dairy no processed foods . And other foods in moderation . . Fingers crossed this will work for me 

Great post! 

when is the essential thyroid book coming out???? I want it NOW!!!!

Hi Claudia, thanks for asking. We hope to have it available Aug. 31. Creating a cookbook is an insane amount of work – more than we’d ever anticipated. 

thank you Jill. I too suffer from Hashimo and from male pattern baldness due to pcos. I have tried everything. I am at a loss... I hope with new supplements my functional doctor has me plus your cookbook I can get better... I am also taking NDT 

I just cannot thank you enough for this! I have beat myself for not being able to stay strict Paleo and feeling guilty for occasionally feeding my family gluten free rice, quinoa or oatmeal. I often feel like a slave to my kitchen because I make everything from scratch. We're going to try your elimnation provocation diet and see what food intolerances we might have and do your gut healing protocol. While I feel the AIP has helped to alleviate the inflammation in my son and his Hashimoto's symptoms, it is extremely restrictive and hard to do with kids. I feel so relieved! Thank you!

I greatly appreciate your point of view however I wonder if you have read Dr. Sarah Ballantyne's book on AIP.  In her books she explicitly states that the strict phase of AIP (phase 1) is to be followed only for a short period of time until your symptoms are under control or as under control as they can be.  There are 4 phases to AIP.  In each stage more and more foods are re-introduced so that you can uncover your trigger foods.  Dr. Ballantyne reccomends at least 30 days in the first phase but states clearly that it may take others a longer period of time to get their symptoms under control..  On her website PaleoMom, she states that many people can do well on a much less restrictive form of even 85/15 AIP once their symptoms are well managed.  By phase 4 of AIP,  you are able to eat dairy, legumes, and non-gluten grains.  She does recommend staying away from gluten permenantly.  Sarah often states throughout her book that it is a personal journey and it is important to find what works for you.   On her website she also states that it isn't about what the paleolithic man did or didn't eat but how your food is affecting your health.   I have been AIP for 8 months, however, the first go round I reintroduced food too fast and had to do another 30 days in phase 1.  I haven't introduced seeds, nuts, grains, legumes, or nightshades back in though I could.  The truth is that  I truly don't miss them. I haven't been successful adding any dairy except for butter back in so I am pretty sure that dairy will never be ok for me.  I have been able to be adventurous in eating and have added so many new vegetables to my life that I am never bored.  I have also found many ways to cut cost including being aware of the Clean 15 things I don't buy organic and the Dirty Dozen things that I always buy organic., finding local providers, making my own coconut milk and growing and canning a lot of my own food.  Yes, I work full time and have a family.  We just make it work.  AIP or not-AIP it is a personal journey but I belelve that as a professional it is important that you represent the AIP diet accurately.  Much of what you say Dr. Ballantyne woul agree with.  I think that many people are like I was.  I tried AIP based on internet research.  It wasn't until I purchased Sarah's book and sat down and read it that I actually understood the full scope of what the AIP protocol is all about.

Lisa, thanks for your comments. The approach that I take also uncovers trigger foods in a systematic way. And given that, depending on the client and their situation, I recommend that they eat only very moderate amounts of grains and legumes, it’s actually similar to the 85/15 you mention. And most people do very well with this approach because we’re doing all kinds of other things to heal their gut and modulate their immune system.

Right, it’s a personal journey. Strict AIP isn’t for everyone – I’m a firm, firm believer in this. And correct, each person has to find what works for them. At this point in my career, over half of my clients have tried strict AIP and either felt worse or didn’t see any improvement. That’s the point of this post. And as I said, I’m not here to discount AIP’s merits. I recommend it in some circumstances. 

So I don’t know what you mean about my responsibility to represent AIP accurately. “Representing” it wasn’t the point of this post and my clients see great results, so again, I’m not inclined to change my approach. But I appreciate you telling me about this book. I’ll look into it.

Thanks for speaking out on this.  Another aspect that hasn't been mentioned is that people with depression and anxiety need carbs to make seratonin. I've tried a strictly Paleo diet and feel well physically on it, but after a month severe depression sets in.  Moderate amounts of whole, glueten-free grains prevents this.  If I'm having a really bad day, then I even allow some simple carbs.  I haven't been retested yet, but I'll be interested to see if just going gluten and dairy free will keep my antibodies down. 

Yes, very true for many. I address this in this post:

Hi there.  This article provided some hope for me.  I'm a 36 year old woman who was diagnosed with Hashimoto's about a year ago after having my first child.  I am so frustrated at this point because my anti bodies are very high (believe it or not, tested recently twice around 6000...yes that's thousand).  I went on AIP for this last month, just had my antibodies tested, and they ARE HIGHER.  What!!! I don't have any big stressors in my life, I don't have any signs of SIBO, barely ever get sick (& if I do, it's a cold that lasts 3-4 days), I have always ate pretty healthy (diet & exercise, average 135 pounds), have given up gluten before & that didn't help either.  I am very discouraged  by how expensive this diet is and it has not been working at all.  I thought I would see SOME result at this point.  

Any advise on a different approach?  I feel like I should maybe get testing to see if I have an underlying infection?  Suggestions please.  

I just feel like it was my last pregnacy where this flared up, and I don't feel like all these other factors are showing relevance to my situation. 

Thank you ahead of time for taking the time to help.

Add comment