The Definitive Guide to the Paleo Autoimmune Protocol (AIP)

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everything you need to know about the paleo autoimmune protocol (AIP)
This article is a little bit more important than usual.

So it’s also a little bit longer than usual. But you should read it all. Especially if you have an autoimmune disease, and probably even if you don’t.

I get a lot of emails from readers asking about the Autoimmune Protocol (often abbreviated “AIP”) within Paleo. Questions like: “What is it?” “Is it right for me?” “How do I do it?” and “Will it help me with ______ problem?”

Unfortunately, there just wasn’t a great article or series of articles that clearly answered all of these questions. And that was a shame.

So…I decided to write this article. It’s a very thorough but easy-to-read guide to AIP, including a comprehensive, printable list of foods that are allowed or not allowed on AIP that you can have emailed to you by clicking below or at the end of the article. There’s also a handy AIP FOOD TABLE below that you can Pin, so keep reading!

What is an Autoimmune Disease?

The first time someone told me they had an autoimmune disease, I thought they meant they had AIDS (yes, I was quite clueless, despite the fact that I actually have an autoimmune disease). For the difference between Autoimmune Disease (AID) and Acquired Immune Deficiency (AIDS), check out this article.

Let me begin by explaining the basics of an autoimmune disease, because the chances are that you might have one!

Autoimmune diseases occur when your body’s own immune system starts attacking your own body’s proteins. This happens because your body thinks that those proteins are a foreign substance (e.g., a bacteria) that need to be destroyed. Unfortunately, this can end up causing widespread destruction of your own organs and cells instead.

There are a ton of different autoimmune diseases (some may not have even been identified, and many of them are obscure like the one I have). Most autoimmune diseases differ based on which proteins/cells are being attacked by your immune system.

Here are some autoimmune diseases you might have come across:

  • Hashimoto’s Thyroiditis
  • Graves’ disease
  • Type 1 Diabetes
  • Rheumatoid Arthritis
  • Psoriasis
  • Celiac Disease
  • Crohn’s Disease
  • Lupus
  • Narcolepsy
  • Ulcerative Colitis
  • Mulitple Sclerosis
  • Guillain-Barré Syndrome
  • Hidradenitis Suppurativa
  • Alopecia Areata
  • Autoimmune Hepatitis
  • Angioedema (what I have)

What Causes Autoimmune Diseases?

The science is still a bit fuzzy on all of the possible causes. However, I’m looking forward to reading Sarah Ballantyne’s book, The Paleo Approach, to get a clearer picture of what’s going on. In any event, one likely possibility is that certain foods we eat can cause our gut to “leak.”

Our intestines are lined with epithelial cells that are designed to keep certain substances out of our body (i.e., they have to remain in our intestine and not pass through the intestinal walls) and to allow other substances in (e.g., certain nutrients). However, certain foods in our diet (in addition to certain genetic predispositions) may cause these epithelial cells to lose their tight structure and thereby open up a gap in the intestinal wall.

Bacteria and dietary antigens could then pass through these gaps, thereby causing our bodies’ immune system to attack them. It’s generally a good thing that our immune system attacks foreign substances (like bacteria) that make it into our bloodstream, since that’s how we fight off illness and infection.

However, the immune response caused by that reaction can also have adverse effects, especially if our immune system is continuously fighting off foreign invaders. One of the main adverse effects is that our immune system often starts attacking other parts of our body, rather than just the foreign invaders. And that’s when an autoimmune disease is born.

What is the Paleo Autoimmune Protocol (AIP)?

The Autoimmune Protocol was original developed by Dr. Loren Cordain and Robb Wolf (see the “Autoimmune Caveat” in The Paleo Solution) as a variation of the Paleo diet to help those with autoimmune diseases.

The idea is to eliminate foods that can “irritate and damage the intestines of some people”, even though these eliminated foods are on allowed on a typical Paleo diet.

There are variations of AIP (in particular, Sarah Ballantyne has come up with a stricter version of AIP), and I’ve drawn up a detailed chart below of the allowed and not allowed foods on AIP, noting the variations.

However, remember that AIP is an eliminate-and-then-reintroduce diet! So, the idea is to eliminate all foods on the “not allowed” list for at least 30-60 days (30 days is generally suggested by most people, but some people do 60 days to make sure – Robb states “a month or two” in his book), and then to re-introduce one food at a time to see how your body reacts.

The idea behind the eliminate-and-then-reintroduce approach is that your body reacts badly with certain (but probably not all) of the “not allowed” foods. However, you won’t be able to tell which ones you react badly to unless you first eliminate all of them very strictly for the 30-60 day period. Elaine from the Phoenix Helix has written a great article on how to reintroduce foods on AIP – you can read it here).

How does AIP differ from Paleo?

For the most part, the 30-60 day elimination component of AIP is a stricter version of Paleo (so you do a pure Paleo diet, and then just eliminate the additional “not allowed” foods for AIP).

Then you spend a few weeks reintroducing the “not allowed” foods back into your Paleo diet.

After you’ve tried to reintroduce all the “not allowed” foods back into your Paleo diet, you will keep doing the Paleo diet and keep eliminating any of the foods that caused you problems when you tried to reintroduce them. For example, if your autoimmune condition worsened when you reintroduced eggs back into your diet after the 30-60 day elimination period, then you would need to keep eggs out of your Paleo diet always even though most people on a Paleo diet eat lots of eggs!

Does AIP work?

I haven’t seen any scientific studies proving the efficacy of AIP, primarily because the concept is relatively new and there’s not a lot of funding for this kind of research. On the other hand, the anecdotal evidence suggests that it works quite well. In fact, Sarah Ballantyne states that AIP “is appropriate for everyone with diagnosed autoimmune disorders or with suspected autoimmune diseases.”

Who Should Try AIP?

Based on the number of people who have emailed me about their autoimmune conditions, I think most people find just sticking to a very pure Paleo diet helps with their conditions. In particular, I’ve heard from a lot of people who have improved their Rheumatoid Arthritis with just a Paleo diet (without attempting AIP).

However, even for those people, AIP may improve their autoimmune condition even more (read Eileen’s story comparing how much better her Rheumatoid Arthritis got on AIP than on the GAPS diet and Tara’s story on how she had to modify her Paleo diet to improve her Hidradenitis Suppurativa).

And for those people (like me) whose autoimmune conditions don’t improve with Paleo, trying AIP is definitely an option to consider! The main downside to AIP is that it is very restrictive, and you have to be very strict during the entire period or you’ll risk going to all that trouble for nothing.

So, if you’re considering doing AIP, make sure to give yourself at least 60 days to test it out (30 days elimination followed by 30 days reintroduction period). Because the diet is so restrictive, it’s best to ensure you don’t eat out at all (or have to travel far) during that period. This has been my biggest deterrent to trying AIP so far (I seem to be traveling all the time!).

Also, be prepared to face the fact that AIP is TOUGH! I’ve always recognized that AIP is tough. I personally have a hard time imagining life without most of the spices I cook with (most of which are nightshades). To that end, reading Eileen’s and Melissa’s accounts have made it all the more real for me.

Common Mistakes on AIP

There are 2 common mistakes that people make on AIP (and also on a normal Paleo diet!):

  1. Thinking You Only Need to Change Your Diet And Nothing Else.
    Most people think AIP (and Paleo) is just a diet. Stress, lack of sleep, and lack of exercise (or way too much exercise for some people) are huge components of AIP that many people miss – in fact, I’m really glad Sarah Ballantyne emphasizes these often forgotten components in her book!
  2. Eating Allowed Foods that You’re Sensitive To.
    Even if a certain food is permitted on AIP, you might still be sensitive to it (e.g., coconut products). So, if you know or suspect there’s something else you should be avoiding, then just treat it as a “not allowed” food and reintroduce it after the elimination period.

Paleo Autoimmune Protocol Food List

Paleo autoimmune protocol AIP not allowed list of foods

I created an 11-page detailed food list PDF for AIP (plus a quick summary list). It’s easily printable and is great as a guide! (It’s just way too long to fit into this article.) So, Click here to have the list emailed to you.

Have You Tried AIP?

Do you have an autoimmune condition? Have you tried AIP before? If so, how did you find it? Let me know in the comments below!

Images: photo credit: maglara, Dmitry Fisher, and Rozmarina.

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{ 12 comments… add one }

  • Alice February 11, 2014, 5:21 pm

    I’m on week 3 now and I think it’s helping with some issues.

    • Louise February 11, 2014, 6:00 pm

      Thanks Alice – that’s great to hear!

  • Faheeza February 17, 2014, 2:33 am

    Hi, I am starting week 4 now and I am still flaring up really badly, I’m not sure if there is something I am missing, let me just make sure with you, is black pepper and white pepper allowed?

    • Louise February 17, 2014, 2:36 pm

      Black and white pepper are typically allowed on AIP, but Sarah Ballantyne suggests eliminating them initially just in case.

  • Jeanne February 18, 2014, 12:03 pm

    I can’t believe you left multiple sclerosis off your list of autoimmune diseases! One of the most well known cases of AIP helping relieve autoimmune disease is Dr. Terry Wahls use of AIP! I see this as a serious omission! You really should educate yourself about the phenomenal Dr. Terry Wahls!

    • Louise February 18, 2014, 2:37 pm

      Hi Jeanne – you’re right I did miss that off the list by accident. I’m familiar with Dr. Terry Wahls and have heard her speak before. She is quite phenomenal, and I’ve recommended her work to many readers. Thanks for spotting that omission.

  • KORINE March 1, 2014, 10:25 pm

    :) Great article!
    I am at week 8 – I have never felt better in my life! I also avoid some ‘AIP Approved’ foods (coconut, some FODMAPS) due to known sensitivities. It is hard, but it is SO worth it! I am going to commence food re-introduction this week, slowly slowly, and fingers crossed I will be able to safely re-introduce some foods to my diet! :)

    • Louise March 2, 2014, 1:21 am

      Thanks Korine – that’s fantastic to hear!

  • Laurelin March 30, 2014, 10:22 pm

    Hi, I am so thankful to have found your site!
    I suffer with Fibromyalgia, severe anemia and seriously depleted B12 due to an inability to absorb it. I am very keen to try the AIP and have tried to access your wonderful list, but when I click the link, I am unable to input my e-mail address as the link is off the page and I can’t seem to realign it properly. Is it possible to e-mail it to me? Thank you!

    • Louise March 30, 2014, 11:34 pm

      Thanks – emailed to you!

  • Cinda April 11, 2014, 9:16 pm

    I’m just 5 days in and ecstatic!!! I have celiac and the last 5 months had nonstop migraines! Life had become unbearable. I started paleo in January, it helped but still was having migraines. I was trying to decide if I should do a Whole30 or AIP. That night I had some chicken curry (with nightshade spices) and woke up with headache….so I went with AIP! Not only is the migraine gone I feel like a cloud has lifted and I’m seeing the sun for the first time in memeory! I didn’t know I could feel this good!

    Big thanks to ALL the pioneers in AIP!

    • Louise April 11, 2014, 11:27 pm

      That’s absolutely fantastic Cinda!


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Louise Yang Ancestral Chef

Hi! I'm Louise - I am "beyond gluten-free," grain-free, paleo/primal, a lawyer, an ex-physicist, a cook, a blogger, a Brit living in the US, an ex-violin player, an occasional crossfitter, a mystery book junkie, and of course, I am the Ancestral Chef :) Read my About Me Page for more!

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