Summary: As the name implies, the Autoimmune Protocol, or AIP, is a therapeutic dietary strategy designed to address autoimmune diseases of all types – including IBD. The AIP addresses both gut and immune health by eliminating all foods that could be immune-activating or disruptive to the gut, and focusing on foods with high nutrient density. The dietary guidelines (including avoidance of grains, legumes, dairy, eggs, nuts and seeds, and nightshades) were already supported by extensive research, but now the AIP as a holistic strategy for IBD is also supported by one uncontrolled clinical trial. Most of my concerns with the diet (specifically surrounding carbohydrate and associated prebiotic content) are being actively addressed by prominent members of the community. As with any strict elimination diet, care should be taken to avoid triggering or exacerbating an unhealthy relationship with food, but overall the AIP is a nutritionally sound diet that has demonstrated success in treating IBD, both anecdotally and clinically.
This article is part of the IBD Index. Last updated on March 22, 2022.
As per my determination to avoid reinventing the wheel, this article primarily consists of links to other resources. The AIP has an extremely robust and scientifically-grounded online community, so while I do hope to one day spend some time comparing/contrasting the various IBD diets (including the AIP), I don’t have much to contribute to the AIP-specific body of knowledge that has not already been contributed by others!
Table of Contents
Who came up with the Autoimmune Protocol?
What is the Autoimmune Protocol (AIP)?
Is there evidence to support using the AIP for IBD?
Are there any risks to the AIP?
Carbohydrate content and prebiotics
Too much insoluble fiber
Food relationship and quality of life
Review of the literature
Who Came Up With The Autoimmune Protocol?
The precise origin of the AIP is slightly hazy, but this post from Mickey Trescott and Angie Alt gives an awesome overview of the history of the protocol (including its key players, books, recipe books, and scientific publications) from 2011 to the present.
From what I can tell, Sarah Ballantyne of The Paleo Mom is the AIP’s primary scientific voice – she holds a PhD in medical biophysics, and wrote the definitive guide to the AIP (The Paleo Approach) which includes over 1200 scientific references and breaks down all the “whys” behind the foods that are eliminated and included on the protocol. Mickey and Angie of Autoimmune Wellness, on the other hand, seem to be the leading players in AIP advocacy and connections, including facilitating clinical trials for the protocol.
What Is The Autoimmune Protocol (AIP)?
For this question, I refer you to Sarah Ballantyne’s excellent and thorough resource: What Is The Autoimmune Protocol? She briefly covers what autoimmune disease is and the different components of the immune system, before diving into a thorough exegesis on the AIP, including a description of included/excluded foods (with links to rationales for each food), the overarching physiological mechanisms involved, the process of elimination and reintroduction, and clinical evidence to date, as well as links to many practical and scientific resources.
If that isn’t enough, Angie and Mickey also have an introductory post on the AIP here. They link to dozens of resources including quickstart and printout guides, definitive guides to special topics like SIBO, guides for cooking and meal prep, budgeting, troubleshooting, mindset, travel, and more.
Is There Evidence to Support Using The AIP for IBD?
Yes! In addition to the extensive scientific research that went into designing the dietary guidelines in the first place (as laid out in The Paleo Approach, mentioned above), the AIP has now been vetted in a first-of-its-kind clinical trial in 15 patients with IBD. For a thorough analysis of that study, check out these articles from Angie and Mickey or Chris Kresser. But in short, the results from the study authors:
“Clinical remission was achieved by week 6 by 11/15 (73%) of study participants, and all 11 maintained clinical remission during the maintenance phase of the study. We did not hypothesize, a priori, that clinical remission would be achieved so early (week 6). Indeed, this proportion of participants with active IBD achieving clinical remission by week 6 rivals that of most drug therapies for IBD…Konijeti, et al. 2017
While these results are impressive, it’s important to bear in mind that this was an uncontrolled study in a relatively small sample.
The researchers go on to say that “importantly, our dietary study was performed as an adjunct to medical therapy, and almost 50% of patients in our study were on biological therapy. Therefore, our results suggest that dietary modification can be used as an adjunct to conventional IBD therapy, even among those with moderate-to-severe disease.”
They also note that the 2 participants with CD with ileal strictures developed either worsening disease activity or partial small bowel obstruction, and they suggest that consideration should be given to anatomical variation and close follow-up is warranted.
All relevant clinical research is linked at the bottom of this article.
Are There Any Risks to The AIP?
Carbohydrate content and prebiotics
Back in 2016 when I was experimenting with AIP, I wrote a post called Getting Enough Carbs on the Autoimmune Protocol. In that post, I say that “given how easy it is to default to a very-low-carb diet on the AIP, I really feel like the carb issue should be addressed more frequently and fully by proponents of the diet.” I muse that many of the issues that crop up when people first start AIP could be due to inadequate dietary carbohydrate, and I link a bunch of posts about potential health issues with low-carb diets. I also give practical advice for where to find weird AIP-compliant carb sources like taro and cassava, how to cook them, etc. I imagine most of the information there is still relevant, so check it out if you’re interested!
I’ll go ahead and pat myself on the back for being ahead of the curve, because it looks like the AIP’s most prominent spokespeople have really come around on the carb issue, and are now intentionally combatting the historical low-carb tendencies of the AIP.
I’ve linked several of their posts on the issue below, but I’d specifically like to call attention to the subsection of this article called “Starch and the Microbiome, Another Reason to Up Carbs” (you’ll have to either ctrl + F or just scroll down to find the section). Sarah Ballantyne discusses how nonstarchy sources of fiber really aren’t adequate to support an optimally healthy microbiome in most people, so it’s important on the AIP to emphasize AIP-compliant sources of soluble fiber like starchy tubers, plantains, and other fruits.
Moral of the story: be aware of the potential risks involved with not getting enough carbs, and arm yourself with strategies to avoid those pitfalls if you’re going to try the AIP.
(Of course, there are situations where carbs should be kept low; for instance, if strategically employing a ketogenic diet.)
Too much insoluble fiber
Related to the above discussion around fiber types, it’s possible that the AIP’s extreme emphasis on nonstarchy veggies could be irritating to an inflamed gut. Alexa Federico, who manages her own Crohn’s disease using the AIP, discusses this and other potential IBD-specific considerations in her blog post here.
Food relationship and quality of life
As with any strict elimination diet, one salient risk is the potential for harming one’s relationship with food or adversely affecting quality of life related to social events, travel, cost, convenience, or other factors. I have not ever been truly plugged into the AIP community, but Angie Alt’s post “AIP is Not a Religion” indicates that AIP is not immune from the intense dietary dogma that I’ve observed in other communities (the Specific Carbohydrate Diet being the most notable example).
As Sarah Ballantyne says on her intro to AIP page,
The AIP is not a life sentence, but rather a toolbox full of strategies for understanding how your body reacts to foods, lifestyle and your environment and methodologies for healing given your individual health challenges.
The AIP is also a holistic approach to health, including not only a dietary framework but also a focus on lifestyle factors known to be important modulators of immune function, gut health, and hormone health. This includes a strong focus on getting adequate sleep, managing stress, and living an active lifestyle while avoiding overtraining.Sarah Ballantyne, The Paleo Mom
In addition to remembering these words, AIP followers should also remember that some people with IBD actually get better following dietary strategies that include – or even depend on – AIP-eliminated foods. One notable example is the bean protocol, which owes its very existence to a food group (beans) that is excluded and even somewhat demonized on AIP.
So if the AIP is working for you – great! But if it’s not, or if it’s adversely affecting your mindset around food or your quality of life in general, remember that you are not only allowed to experiment with other options, but that trying other strategies may very well be the best thing for you.
All posts linked in this article in order of appearance:
The History of the AIP Movement (2011 to present) from Autoimmune Wellness
What Is The Autoimmune Protocol? from The Paleo Mom
About AIP from Autoimmune Wellness
AIP Medical Study Results from Autoimmune Wellness
AIP for IBD: The Paleo Autoimmune Protocol and Inflammatory Bowel Disease from Chris Kresser
How Many Carbs Should We Eat? from The Paleo Mom
The Case for More Carbs: Insulin’s NonMetabolic Roles in the Human Body from The Paleo Mom
AIP FAQ: Carbohydrate Intake on the Autoimmune Protocol from The Paleo Mom
The Ultimate Guide to Managing IBD with AIP from Alexa Federico
AIP is Not a Religion from Autoimmune Wellness
Review of the Literature
Because there are only a small handful of AIP studies out there, I’ve included all of them below: first the IBD-specific ones, then the others. Note that a study on AIP for eczema is currently in progress – I’ll add that once it’s published!
Note that the first reference is the primary paper from the first study on AIP in IBD: an uncontrolled trial in 15 IBD patients (9 CD and 6 UC). The two papers listed after that are substudies or additional analyses from data collected during that one study. The fourth paper describes results from a survey from the same research group.
Konijeti et al. Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Disease. 2017. Inflamm Bowel Dis.
- Clinical remission was achieved by week 6 in 11 of the 15 (73%) study participants, and all 11 maintained clinical remission during the maintenance phase of the study
- Detailed reviews of results from Mickey and Angie and from Chris Kresser
Chandrasekaran et al. The Autoimmune Protocol Diet Modifies Intestinal RNA Expression in Inflammatory Bowel Disease. 2019. Crohns Colitis 360.
- This was an RNA substudy within the above primary study in four participants with UC (taking mesalamine) who underwent both pre- and post-AIP colonoscopy or sigmoidoscopy
- We observed modulation of pathways involved in inflammation, DNA repair, metabolic processes, and cellular proliferation, suggesting cellular responses to dietary modification
Chandrasekaran et al. An Autoimmune Protocol Diet Improves Patient-Reported Quality of Life in Inflammatory Bowel Disease. 2019. Crohns Colitis 360.
- This paper presents the quality of life analysis of the data collected during the primary study
- Our study suggests that the AIP diet has the potential to significantly improve QOL within a relatively short time frame, including during the elimination phase of dietary therapy. Effects were also sustained during the maintenance phase. The data suggest the clinical benefits are similar in both CD and UC patients, regardless of current IBD medication use. Therefore, the AIP diet, similar to other elimination diets, has the potential to be an effective adjunct to conventional IBD therapy.
Lee et al. Clinical Course and Dietary Patterns Among Patients Incorporating the Autoimmune Protocol for Management of Inflammatory Bowel Disease. 2019. Curr Dev Nutr.
- An anonymous online survey (78 total respondents) was sent through electronic newsletters and support groups utilizing AIP to assess demographics, disease activity, medication use, and dietary adherence
- Patients utilizing AIP for management of IBD report clinical benefit of AIP, reduction of steroid use, and successful food group reintroduction
Other AIP Studies
Abbott et al. Efficacy of the Autoimmune Protocol Diet as Part of a Multi-disciplinary, Supported Lifestyle Intervention for Hashimoto’s Thyroiditis. 2019. Cureus.
- Sixteen women with HT completed a 10-week online AIP program that coached them on implementing the diet
- At the end of the 10 weeks, there was a statistically significant improvement in health-related quality of life and a 29% reduction of inflammation (measured by hs-CRP; from an average of 1.63 mg/L to 1.15 mg/L)
- No improvement was observed in any measure of thyroid function
Leave a Reply