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Autoimmune paleo protocol in Inflammatory Bowel Disease – clinical study shows remission in 73%


This study set out to test whether the auto-immune paleo diet can help people with inflammatory bowel disease.

Inflammatory Bowel Disease (IBD) comprises of a group of intestinal disorders, the main two being Crohn’s disease (CD) and Ulcerative Colitis (UC). These are characterised by chronic, relapsing inflammation of the gastrointestinal tract. This inflammation is thought to be the result of an excessive immune response to antigens of normal gut microbiota.

IBD rates increased rapidly across the Western World from 1940 to 1980. It is thought to be related to changes in gut microbiota.

Despite many anecdotes of people reporting that a paleo or autoimmune paleo protocol helps with inflammatory bowel disease and other auto-immune conditions, there have been very few clinical studies to test it.

Without clinical studies we have no idea as to what percentage of people may benefit, and what percentage get no or even a detrimental result. The problem with anecdotes is that we hear success stories, people who try the diet, get relief, then talk about their experience. Those who tried it and did not get success are more likely just to move on and stay quiet.

A clinical study testing the efficacy of the paleo auto-immune protocol in a group of people with IBD is the only way to find out how many improve, and how many don’t.

This study was published late last year:

Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Disease

Here is an outline of the study and results

The AIP diet used in the study

Auto-immune paleo protocol (also referred to as AIP)

The AIP diet is an extension of the Paleo diet, and removes extra foods that are can trigger intestinal inflammation.

Standard paleo diet removes:

  • Cereal grains, e.g. wheat, rye, barley, corn, oats, etc
  • Grain like seeds, e.g. buckwheat, quinoa etc
  • Legumes and lentils, including soy and peanuts
  • Dairy products, e.g. milk, cheese, yoghurt
  • Processed foods, primarily because of additives like emulsifiers, fillers, colours, preservatives and flavours
  • Sugars
  • Refined seed oils

An auto-immune paleo diet removes further foods:

  • All nuts
  • Eggs
  • All seeds including seed spices, coffee and cocoa
  • Nightshade group of vegetables: eggplant, potatoes, tomatoes, peppers
  • Alcohol
  • Additives
  • Non-steroidal anti-inflammatory drugs that cause inflammation to intestine if possible

The rationale for removing all the foods is to remove foods that promote intestinal inflammation and permeability, dysbiosis, and foods that are those to which people are most often allergenic or intolerant.

Foods added to a paleo diet

Paleo is not just food removal, it is also important that nutrient dense foods are added, as well as foods that nourish to promote a healthy gut and decrease inflammation:

  • Fresh nutrient dense foods- from animals, seafood and plants
  • Bone broth
  • Fermented foods

Lifestyle factors matter too

The paleo or AIP diet is not only a diet protocol – it also emphasises lifestyle that improves health, and is known to reduce factors that impact auto-immune disease and IBD

  • Sleep and sleep hygiene
  • Stress management
  • Physical activity
  • Supportive relationships

Participants in the trial

Adults who were 18 years or over, with symptomatic ulcerative colitis (UC) (partial Mayo clinic score of 3 or more)  or Crohn’s Disease (CD) (Harvey-Bradshaw index of 5 or more) They also needed to have had an endoscopy and visible evidence of disease in the previous 7 months, or an elevated calprotectin (>50ug/g). Medication during the study was to stay stable, with the exception of corticosteroids, which could be tapered off.

Eligible patients were enrolled through the Scripps Clinic Medical Group Division of Gastroenterology (La Jolla, CA).

Eighteen patients were enrolled in the study, 15 completed, 9 with CD and 6 with UC.

The mean length of time that participants had their disease was 19 years.

Medical Tests

Medical tests were done at baseline, 6 and 11 weeks to assess gut mucosal healing, and measure inflammatory biomarker changes.

Vitamin D and Iron repletion

Before the study started particpants were tested for vitamin D and iron levels, and if low these were rectified with supplements.

Dietary Intervention

Elimination phase of diet

The elimination phase is a staged removal of grains, legumes, nightshades, dairy, eggs, alcohol, nuts and seeds, refined processed sugars, oils and food additives.

The protocol followed in this study was the “SAD to AIP in 6” https://sadtoaip.com an online programme that guides participants through the diet changes over 6 weeks, gradually taking out and replacing foods.

Once all the non AIP foods are removed,  the diet is maintained until there is a measurable improvement in symptoms and overall wellbeing. In this study there was a 5 week maintenance phase.

Support was provided, a health coach and a dietitian, as well as fellow participants via a closed Facebook group.

The participants also received a copy of “The Paleo Approach” by Sarah Ballantyne and “The autoimmune paleo cookbook” by Micky Trescott.

Food Re-Introduction Phase

This phase took place at the end of the study and participants were given guidance on re-introduction of food groups. This is a staged process, to identify individual foods or food groups that may contribute to symptoms. Foods that do not cause any untoward reaction can be kept in the diet.

Study Goals

The goal of the study was to evaluate the effect of AIP on UC and CD, and find out what proportion of them went into remission.


At week 6, 11 people of 15 achieved remission, 6 out of 9 with CD and 5 out of 6 with UC, that is 73% of participants. All 11 participants stayed in remission in the 5 week maintenance phase.

Two participants worsened, one had a small bowel obstruction as a result of the diet change, which resolved quickly with treatment,  and one had an increase in faecal calprotectin (a measure of inflammation in the gut).

Below are the study results from the paper

If you look across and compare week 0 to week 6 and 11, you can see significant reductions in markers of disease.

This study can be viewed as a pilot study and to confirm whether an AIP diet would be a great intervention for IBD, further larger studies with a control group would be needed.


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