The first scientific study of the Autoimmune Protocol (AIP) was conducted last year and the results were published this month in the journal Inflammatory Bowel Diseases.

Those results have created quite a buzz.


73% of participants achieved clinical remission of the symptoms of Crohn’s Disease or Ulcerative Colitis within six weeks.

That sounds amazing. What does it mean?

It means that most participants experienced substantial healing after a six-week process of gradually transitioning to the Autoimmune Protocol.

What is astonishing about these findings is that it is only at the six-week mark that these study participants were actually fully in the elimination phase of the AIP. Normally that would be the point at which we’d start counting the weeks (or months) to measureable improvements in autoimmune symptoms.

So yes: amazing.

Inflammatory Bowel Disease

This study included 15 participants. Nine with Crohn’s Disease and six with Ulcerative Colitis.

Crohn’s Disease and Ulcerative Colitis are two autoimmune conditions that both fall under the umbrella of Inflammatory Bowel Disease.

Symptoms of Inflammatory Bowel Disease include extreme diarrhea and abdominal pain, fatigue, rectal bleeding and, in some cases, narrowing of the intestine (called a ‘stricture’) which can slow or block movement of food through the digestive tract.

According to experts, people with Inflammatory Bowel Disease find their symptoms “embarrassing and humiliating. IBD can result in loss of education and difficulty in gaining employment or insurance. It can also cause psychological problems and growth failure or retarded sexual development in young people. Medical treatments such as corticosteroids or immunosuppressive drugs cause secondary health problems, and surgery may result in complications such as impotence or intestinal failure.”

These are serious illnesses.

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Crohn’s Disease

Crohn’s Disease involves inflammation of any part of the digestive tract, including the small and large intestine. It can sometimes also affect the mouth, esophagus, stomach and anus.

Ulcerative Colitis

Ulcerative Colitis is kind of like it sounds. Ulcers. In the colon.

Those of us who don’t suffer from it, can take a moment to imagine how painful that would be.


The standard treatment for Inflammatory Bowel Disease includes a rotation of various drugs, many of which have pretty serious side-effects. Especially after long-term use.

Most of the participants in this study had been living with Inflammatory Bowel Disease for more than a decade (19 years on average). They had tried pharmaceutical and surgical treatments, without remission of symptoms.

Which is what makes the results of this study even more remarkable.

The Autoimmune Protocol

The elimination phase of the Autoimmune Protocol (AIP) is a strict version of the paleo diet, with additional lifestyle components. Matthew and I started the AIP in 2013 and that was what finally enabled Matthew to get traction on his healing.

You can find more information about the AIP here.

Yes: we already know it works

Thousands of people all over the world have found that they can manage, and even reverse, the symptoms of diverse autoimmune diseases using the AIP. But these results, no matter how compelling, are just anecdotal.

'Anecdotal’ means that they have not been proven scientifically. And therefore can be ignored by the medical community.

That is why this study is such a big deal.

Even though thousands of people have experienced similar results, these particular results have been documented scientifically and published in a peer-reviewed journal.


Angie Alt, one of the earliest adopters of the Autoimmune Protocol (even earlier than Matthew and I) designed the SAD to AIP in SIX program to facilitate the transition to the AIP over six weeks.

This program is offered online by health coaches who support the process of:

  1. Removing all inflammatory foods and replacing them with foods that include the necessary properties, including micronutrients, to support healing; and
  2. Incorporating the lifestyle components of the AIP through improving sleep, incorporating appropriate movement, adding stress-management practices, and prioritizing healthy social connection.

Late in 2015, Dr Gauree Konijeti, Director of the Inflammatory Bowel Disease Program Division of Gastroenterology at Scripps Clinic in California, approached Angie about using her program to conduct a medical study of the AIP to evaluate its efficacy for patients with Inflammatory Bowel Disease. Angie enthusiastically agreed.

SAD to AIP in SIX runs a number of times per year. The next session starts in January 2018.

The Study Results

Beneficial Results

  • 73% of participants (11/15) achieved clinical remission of symptoms by the end of the six-week transition to the Autoimmune Protocol. All eleven maintained clinical remission for the remainder of the study (an additional five weeks on the elimination Phase of the AIP).
  • Clinical remission occurred for participants with both Crohn’s Disease (6/9) and Ulcerative Colitis (5/6).
  • Rectal Bleeding was “significantly reduced” for study participants with Ulcerative Colitis.
  • Though Dr Konijeti and her team advised no medication changes during the experiment, a number of participants discontinued pharmaceutical treatments during the study as a result of improved symptoms.

Adverse Results

  • Of the 18 people who originally qualified to participate, three decided not to participate due to “inability to commit to dietary change”.
  • Two of these original 18 participants had ileal strictures (narrowing of the lowest part of the small intestine), and both withdrew due to complications. One withdrew due to worsening symptoms. The other was treated for an intestinal obstruction at the 3-week mark. The symptoms resolved overnight, but the participant dropped out of the study at that point anyway.


All studies have limitations.

The biggest limitation of this study, from my perspective, is that it explicitly credits dietary changes for the improvements in participant’s health (the title is Efficacy of the Autoimmune Protocol Diet for inflammatory Bowel Disease), when the AIP is definitely a nutrition + lifestyle approach.

SAD to AIP in SIX eases people in to the nutrition and lifestyle changes of the AIP over six weeks and there is no way to tease out the diet component and credit it alone for the positive results participants experienced.

Authors also noted that the small size of the study as a limitation.

However, here at Biohack U, we are all about experiments with one participant (n=1), so we’re fine with that. As are (I’m guessing) the eleven people who experience rapid resolution of their symptoms in six short weeks.

Featured Resource

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Want to start seeing results with your own autoimmune healing?

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Whether you are going straight to the elimination phase of the Autoimmune Protocol or need to take your healing in stages, the Autoimmune Healing n=1 Workbook Kit can help you find your best path. Starting where you are right now.


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