What is the Autoimmune Protocol Diet? & Does It Actually Work?

Anna Autoimmune Mom (& Dad) Life, Disease Management & Treatment, Food is Medicine, Healing Kitchen & Diet Tips, Living Well with Autoimmune Disease Leave a Comment

This is Part 1 of our Autoimmune Protocol (AIP) Diet series.  The other posts in this series include:

Part 2: Does the Autoimmune Protocol Diet Work? A Deep Dive into My Personal Experience

Part 3: 7 Major Mistakes I Made on the AIP Diet (& the 3 Things I Did Right)

honey stick and avocado with text overlay - Autoimmune Protocol Diet: What is the Autoimmune Protocol (AIP) Diet? & Does it Actually Work?Welcome to the confusing world of healing diets for autoimmune disease.  In case you haven’t been here before, there are MANY diets to choose from.  And sometimes it feels like you’re throwing darts at a dart board – hoping you land on the right one.

I’ve been there, friend.  In fact, I’m still there… my diet changes with every season of life it seems.  But, for the past couple years, me and the Autoimmune Protocol have really hit it off.  Every once in a while, we go our separate ways, like long lost high school friends, but then somehow (usually due to a mini-flare), we reconnect and it’s like we never skipped a beat. 

That isn’t to say it’s always been like that.  No.  We’ve had our share of ups and downs.  And in this blog series, I’m going to talk about them.

Before we get to that, let’s first discuss the basics…

What is the Autoimmune Protocol Diet?

The Autoimmune Protocol Diet (sometimes referred to as the Autoimmune Paleo Diet, or the “AIP” diet) is a diet created specifically for managing and possibly reversing… you guessed it, autoimmune diseases. 

This is not the typical calorie-restricting or weightloss diet.  Instead, it is a healing diet that focuses on removing all potentially inflammatory & allergenic foods and replacing them with the most nutrient-dense & nourishing foods.

By doing this, you calm your over-stimulated immune system and give it a clean slate while potentially resolving many of the underlying root causes behind autoimmune disease… such as:

-Leaky gut

-Hormone dysfunction

-Nutritional deficiencies

-Food sensitivities, allergies, and other immune system triggers

-Various infections

-Impaired detoxification

After following the elimination phase of the diet 100% (strict, no cheating… for real) for 30 days or longer, depending on how you’re feeling, you begin reintroducing foods one by one using a specific protocol/list to see if they give you inflammatory responses/symptoms.  If a certain food gives you an undesirable response, then you know your body can’t tolerate that food (at least for now).

Once you’ve reintroduced all the foods, or feel comfortable with the list of foods you tolerate well, you are left with a completely customized diet plan for YOUR body.  Not your mom’s.  Or you neighbor’s.  This really is what works for you.


But, it’s more than just a diet.

Of course, the main foundation of the Autoimmune Protocol is diet, but that’s only a piece of the overall picture.  It’s hard to heal from anything if you’re only sleeping 4-5 hours a night or are exposed to constant, chronic stress, whether you choose to be or not. 

Therefore, the Autoimmune Protocol is a total diet AND lifestyle makeover, with the intent to use these as tools to manage your autoimmune condition and live a happy (and hopefully symptom-free) life.

So, what foods can you eat/not eat?

The first phase of the diet is the elimination phase, which removes all potentially inflammatory foods.  Brace yourself for this list.  It’s a doozy, especially if you’ve never heard of the AIP diet before.

Foods Eliminated on the Autoimmune Protocol Diet



All processed foods, preservatives, artificial ingredients

All grains and psuedograins (like quinoa)

Legumes (soy, beans, lentils, chickpeas, peanuts, etc.)


Nuts and Seeds (even chia & flax)

Spices made from seeds (such as coriander, cumin)

Highly refined, processed oils


Chocolate (so sad…)

Thickening gums (like acacia or guar gum)

Emulsifiers (such as soy lecithin)


Alternative sweeteners (not even stevia)

Nightshade vegetables (tomatoes, eggplant, peppers)

… I think that’s it.

Crazy, right?  And I thought going gluten-free was hard!  Ha… so, given this list, what foods are we left with?

Foods Allowed on the Autoimmune Protocol Diet

Meat, poultry, seafood with an emphasis on the grass-fed/finished, wild-caught varieties, and organ meat

Vegetables (except for the nightshades)

Coconut products, including coconut milk, coconut flour, shredded coconut, coconut aminos (a soy sauce alternative), etc.

A few different types of alternative baking flours such as green banana flour, cassava flour, and tigernut flour (which is known as tuber, not a nut)

Carob (a chocolate alternative – colored and cooks the same, does NOT taste the same)

Fermented foods

Grass-fed collagen and gelatin

Unrefined sweeteners such as maple syrup and honey

Herbs (as long as they aren’t seed-based herbs)

Green tea

Bone broth

Healthy fats (avocado oil, olive oil, coconut oil, animal-rendered fats such as lard, tallow, fish oil, etc.)


If the list sounds short, that’s because… it is!  But, I have to say – it’s surprising how many different types of meals and treats you can make using these foods.  I used to think this diet was depriving me, (one of the many AIP diet mistakes I talk about in this post) but I changed my outlook once I got a little more creative with food prep.  Plus, the diet is not meant to be for forever… so that is important to keep in mind.

So that covers the bare-bone basics.

The reasoning behind why all of these foods are eliminated and all the other foods are emphasized is kind of intense.  There is literally an entire textbook written about it with all of the supportive super-detailed scientific literature. 

If you really (I mean REALLY) want to dive deep the science behind this diet, then The Paleo Approach by Dr. Sarah Ballantanye is the book for you.  You can also read her plethora of detailed articles on her blog: The Paleo Mom.

If you want a more summarized resource, The Autoimmune Wellness website is a wise place to start… as well as their book: The Autoimmune Wellness Handbook, which I did a review of in this post.

Now onto what y’all really care about…

Does the AIP diet actually work?

Like anything in life involving health and humans: it depends.  It especially depends on how you define “work” or success.

Let’s take a look at one of the most recent AIP medical studies done on women with the autoimmune disease: Hashimoto’s Thyroiditis – a common autoimmune disease that attacks the thyroid gland.

In this study, 17 women between the ages of 20-45 followed the popular SAD (Standard American Diet) to AIP in SIX program, which took them through a transition from the Standard American Diet to the AIP diet.  The course of the study was 10 weeks long.  Various markers were measured including: quality of life (using the SF-36 Quality of Life Questionnaire), symptom burden, thyroid function, and inflammatory & autoimmune markers related to Hashimoto’s.

Here are some of the results taken directly from the Autoimmune Wellness website:

  1. 16 of the 17 women finished the study.  1 woman got pregnant (her goal!) and could not finish the study.
  2. All 8 subscales of the SF-36 Quality of Life questionnaire improved dramatically over the 10-week program.  The biggest improvements were seen in physical functioning, energy, mental health and even bodily pain!
  3. Symptom burden decreased dramatically over the 10-week study with major improvements seen in energy, joint and muscle pain, digestive symptoms such as constipation/diarrhea, and bloating as well as improvements in mood and cognition.  Many individuals reported improvement in skin conditions such as eczema, acne, hives and dry skin.
  4. Many of the individuals reported improvements in sleep and ability to exercise/increase movement.  Many began formal meditation and stress reduction practices.
  5. Inflammation as measured by the marker hs-CRP decreased by 30% over the 10-week study!  There was also a notable decrease in white blood cells, which likely indicated improvements and balance to the immune response.
  6. 6 out of the 13 women on thyroid medication decreased their medication by the end of the 10-week program.  The 3 women who began the study without the use of hormone replacement continued without the use of medication at the end of the study.
  7. Many individuals saw improvements in nutritional status as measured by markers on the organic acid test.  This included improvements in vitamins such as B6, B12, and riboflavin.
  8. There was some indication that certain individuals needed to consume more folate as part of the elimination phase of AIP.  We believe this emphasizes the importance and need to consume organ meat beyond leafy greens and other sources of folate during the elimination phase of AIP, when certain folate dense food sources are removed.
  9. There were no changes in thyroid hormone or thyroid antibody markers when evaluated across the group, however, some individuals saw decreases in TSH values that necessitated the use of less medication and some individuals did see decreases in thyroid antibodies over the 10-week study.
  10. An online community, involving both functional health coaches and a functional physician, as well as the gradual nature of the AIP eliminations improved collective adherence to the strict AIP diet dramatically.

You can read a more detailed breakdown of the study in this post:

AIP Hashimoto’s Medical Study Results

If you don’t want to read, you can also listen to this podcast:

A New Study on Hashimoto’s Disease, Diet, and Lifestyle

Now, let’s talk about it.

Of course, this is only one study with a small group of women, so take it for data not fact.  But, overall… the AIP diet made a dramatic different in these women’s lives! 

Just take a look at that decreased symptom burden and increased quality of life.  For so many of us, that’s all we are asking for… right?  Just to be able to do normal things every day without extreme ultra-mega exhaustion and pain.  So, from that standpoint, I’d say the AIP diet was a major success.

However… those tricky thyroid antibodies didn’t budge much for the group as a whole.  And someone might look at that and think the AIP isn’t all that effective because it didn’t actually reverse the disease… if you feel that way, then please read this article which goes into deeper detail about the limitations of the study and why antibody levels don’t necessarily correlate with success/failure.

On a side note, I was not one of the women in the study, but what I can tell you is that my personal experience demonstrated that the AIP diet AND lifestyle, paired with a functional medicine approach, significantly reduced my thyroid antibodies down to almost zero and kept them there.  (You can read more about that journey here.

10 weeks is really NOT a long time.  I’d be curious to see antibody levels after about a year or so following the program.

Anyways, given the results – you be the judge… did the AIP diet work?

Before you make your final judgement though, read:

AIP Medical Study Results: IBD (including Crohn’s and Ulcerative Colitis) and More AIP IBD Medical Study Results.  (I think you’ll be impressed.)

There are also more studies coming!  Keep an eye out for the results from the AIP and Eczema/Psoriasis Study currently underway.  I’m excited to see if they align with our personal experience using the AIP diet to calm our daughter’s eczema.

Now, it seems we have arrived to my intended purpose of this post, which is whether or not the diet worked for me personally.  I’ve already dropped a few hints about my experience with this diet, but there’s much more to it, and this blog post turned out to be way longer than expected… so I am now going to turn this into a series.

The next post (Part 2) is a detailed rendition of my first and second experience with a full 30-day strict AIP diet.  Click below to read:

Does the AIP Diet Work? My Personal Experience


honey stick and avocado with text overlay - Autoimmune Protocol Diet: What is the Autoimmune Protocol (AIP) Diet? & Does it Actually Work?

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