Episode 118 – Autoimmune Protocol Diet

Key Topics Covered

Autoimmune Protocol Diet Foods


  • There is a lot of information out there on this diet and it can be confusing on what to trust.
  • It’s a pretty nuanced topic and it’s definitely worth doing a deep dive.

What Are Autoimmune Conditions?

Normal immune response vs autoimmune - 'verywell fit'

  • In autoimmune conditions, the body mistakenly attacks its own tissues.
    • This causes damage and can lead to a whole host of issues. 
  • Autoimmune conditions have a broad range of categories, but some common ones include inflammatory bowel disease, Hashimotos, Lupis and rheumatoid arthritis.  
  • They are all individual conditions, but the information in this podcast is meant to be broad.  

What Is the Theory Behind the AIP Protocol Diet?

  • The AIP diet, as you can tell from the name, is targeted at all autoimmune conditions so it is not specific  
  • The AIP diet is designed to reduce inflammation in the gut and heal the immune system and the gut lining. It is also meant to improve the gut microbiome.
  • Part of this is based on the theory that a lot of autoimmune conditions have a link with ‘leaky gut’. A 2020 Narrative Review explores this link. 

What Are the Specifics of the AIP Diet?

  • It’s largely based on paleo, but the elimination phase is even more rigid.
  • Like most elimination diets it follows the phases of: Elimination -> Reintroduction -> Maintenance/Personalisation.
  • One difference is that it won’t solve the issue entirely, but may reduce symptoms.
  • Theoretically, you eliminate a bunch of foods, then your symptoms improve significantly. Then when you systematically reintroduce foods, you will identify what triggers symptoms. 
  • If you don’t see symptom improvement within 2-3 weeks, the diet didn’t make a difference and it is fine to stop. 
  • There are different variations of the diet too.
  • It is also designed to be particularly nutrient-dense.  
Fine to Eat Avoid at First 
Nose-to-tail grass-fed or wild-caught animal proteins, including meat, fish, fowl, organ meats, and bone broth All grains, eggs, and legumes, such as green beans, black beans, white beans, kidney beans, and garbanzo beans 
Healthy fats and oils such as coconut oil, olive oil, avocados and avocado oil, and coconut milk All nuts and seeds, such as almonds, walnuts, and chia seeds, including their derivatives like seed oils and vegetable oils; for example, canola oil, walnut oil, and almond flour 
A wide variety of fresh fruits and veggies, including sweet potatoes, greens, lettuce, cucumbers, zucchini, berries, apples, and melon Nightshade vegetables, including tomatoes, potatoes, peppers, eggplant, tomatillos, and spices derived from nightshades, like paprika and cayenne pepper 
Non-dairy fermented foods, including sauerkraut, kombucha, and kimchi All dairy products, including ghee, kefir, milk, cheese, and cream 
Herbs and spices not derived from seeds, such as cinnamon, turmeric, thyme, oregano, basil, and rosemary Spices derived from seeds, including fennel, cumin, dill, anise, mustard, coriander, and nutmeg 
Stevia and maple syrup Most added or artificial sweeteners and food additives, plus alcohol and coffee 

Summary of Leaky Gut

how does leaky gut work?

  • Before exploring the research, it’s important to provide a summary of ‘leaky gut’ since this is the foundation of how this diet is proposed to be helpful for autoimmune conditions.
  • Leaky gut as a stand-alone diagnosis is quite controversial. In the medical field, it is not recognized BUT it is among naturopaths and homeopaths.
  • Regardless of whether leaky gut can be a diagnosed condition, we do know that intestinal hyperpermeability is a real thing.

Intestinal hypermermeabiity

  • The digestive tract is where food is broken down and nutrients are absorbed into the body’s circulatory system. 
  • The human digestive system tightly regulates what passes through into the blood. 
  • Small gaps in the intestinal walls, called tight junctions, allow water and nutrients to pass through. But they typically stop larger particles such as bacteria and toxins from passing.  
  • When intestinal hyperpermeability is present, the tight junctions are not as tightly regulated as they should be. These larger particles are able to pass through the intestinal wall and into the bloodstream.  
  • The leaky gut theory proposes that a more permeable bowel lining can lead to many issues including issues with the immune system  

Research on the AIP Diet

research papers

  • There are really only 3 relevant studies on this topic. The diet has been popularised since around 2011/2012. Paleo has been popular since around 2002. So that adds a bit of context around the research we specifically have on this.  

Study 1 – ‘Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Disease’

  • This is a 2017 study conducted over 11 weeks involving 15 people with IBD following an AIP diet.
  • Participants reported experiencing significantly fewer IBD-related symptoms by the end of the study. However, no significant changes in markers of inflammation were observed
  • Of those 15 people, 3 had vitamin D deficiency and 6 had iron deficiency. These nutrients were supplemented as well. 
  • Participants were also given two books. One was ‘The Paleo Approach’ by Dr Sarah Ballantyne. The other was ‘The Autoimmune Wellness Handbook’ by Mickey Trescott.  
  • Clinical remission was achieved in 6 weeks (which was the elimination phase) in 11 of the 15 participants. That’s 73%. 
  • ALL participants experienced improvements in their symptoms, even if remission wasn’t achieved

Study 2 – ‘An Autoimmune Protocol Diet Improves Patient-Reported Quality of Life in Inflammatory Bowel Disease’

  • This study had another 15 people with IBD follow the AIP diet for 11 weeks (6 weeks elimination, 5 weeks maintenance).
  • Participants reported significant improvements in bowel frequency, stress, and the ability to perform leisure or sport activities as early as 3 weeks into the study. 

Study 3 –  ‘Efficacy of the Autoimmune Protocol Diet as Part of a Multi-disciplinary, Supported Lifestyle Intervention for Hashimoto’s Thyroiditis’

  • This is a 2019 study that had 16 women with Hashimotos follow the AIP diet for 10 weeks. 
  • By the end of the study, inflammation (CRP) and disease-related symptoms decreased by 29% and 68%, respectively
  • Participants reported significant improvements in quality of life.  
  • NO changes in measures of thyroid function were observed. T3, T4, and thyroid antibodies remained unchanged. 

Reasons NOT to Do AIP  

  1. It’s restrictive. This could have issues for social eating and/or disordered eating cases.
  2. Although it is a nutrient-dense diet, if you are limited with food choices in combination with limited food preferences (e.g. fussy eating) this could make it hard to get sufficient calories/macros/micros, which could cause issues.  
  3. We also see benefits from other dietary changes.
    • For example, a 2020 systematic review on nutrition for lupus found that a low-calorie, low-protein diet, high in fiber; omega-3 and omega-6 polyunsaturated fatty acids; and vitamins A, B, C, D, and E; as well as calcium, zinc, selenium, iron, copper, and polyphenols, improved symptoms and quality of life for lupus patient
  4. There is limited research & no guarantee it will work.  
  5. Those who find benefits might be reluctant to try to reintroduce foods and maintain a very restrictive diet long-term.  
  6. Due to a lack of research, there is a lot still unknown. Some of it could be based on unfounded logic. For example, some of the foods that are cut out to limit inflammation might not cause inflammation in the first place.  
  7. There are also some flaws in the paleo diet in general.

Reasons TO Do AIP 

  • All of the studies we have looked at, both published and unpublished research, show improvements.
  • Trial and error is often involved in autoimmune conditions. This is one way of doing that elimination and reintroduction process. 
  • Outside of the restriction aspect, there is minimal downside to trying it.  
  • It is also nutrient-dense

Dr Sarah Ballantyne mentions in her writing and presentation that in autoimmune conditions, the body is ‘STARVED’ for nutrients. 

  • This wording is probably not that accurate, but we do see a lot of common micronutrient deficiencies being linked with autoimmune conditions.
  • Following a nutrient-rich diet is a great place to start as it will indirectly address a lot of that without you needing to try to identify each individual deficiency. 
  • The diet has a large emphasis on offal / organ meats / connective tissue 3-5x per week, which contributes to this. 


  • From one perspective, the research we have so far is promising. Particularly since the majority of the participants in these studies have noticed improvements. 
  • It is also not a permanent diet, so worst-case scenario, you try it, it doesn’t change anything and you go back to what you were doing or try something else.
    • Best case scenario, it does help and you complete the reintroduction process.
  • From the other perspective, we have minimal research. These studies aren’t exactly placebo-controlled type studies either e.g. they are receiving books etc. that make them buy into the system more. 
  • Personal opinion: It’s been an option since 2011/2012. Using rheumatoid arthritis as an example: If this was having huge success, in large sample sizes, we would be hearing more about it and it would be more mainstream. More research would also be done.  
  • The lack of changes in certain markers is important. The people who promote this diet acknowledge that and state the obvious point that we care about symptoms and quality of life more.
  • But if there is zero change in thyroid markers for example, for somebody with Hashimoto’s, that is also worth paying attention to.  

Relevant Blogs / Resources

Studies Mentioned  

Blog Posts