I’ve recently had a lot of patients tell me they’ve started the Autoimmune Protocol (AIP) Diet, and have experienced good results. So I decided to look into it a bit more. Here’s what I’ve found.

Autoimmunity: What it Is

As I discuss here, autoimmunity always goes back to the gut. So it makes perfect sense to address it at the level of the gut. I’m very much on board with that idea. The foods that I restrict in cases of autoimmunity are those that will perpetuate gut inflammation—at least for the 6 weeks or so that it generally takes in order to heal up the gut lining.

The AutoImmune Protocol Diet

The Autoimmune Protocol is essentially paleo, which means no grains, no legumes (beans, lentils, etc), no dairy, and nothing refined (sugars, processed veggie oils, or food chemicals).

In addition to this list, the AIP restricts eggs, nuts, seeds, veggies in the nightshade family (potatoes, tomatoes, eggplants, and peppers), and any food with gluten cross-reactivity potential.

What you should eat instead on this diet: grass fed meats and organ meats, lots of seafood (wild caught or otherwise), as many veggies as you can cram in (with the exception of nightshades), fermented foods, and bone broth.

There are a few other delineations in terms of spices as well.

My Take on Restricting Grains:

I certainly have some patients whose guts are so inflamed that they cannot tolerate grains at all, including starchy veggies like potatoes. These tend to be SIBO patients or patients with Irritable Bowel Disease, such as Crohn’s or Ulcerative Colitis, for the most part, and this is one reason why they do best on the Specific Carbohydrate Diet. The reason for this goes back to the “vicious cycle” of inflammation, as described by Elaine Gottschall. That explanation goes like this:

Think of carbs as sugar (which essentially they are—your body converts them into sugar). Your body can absorb simple (single) sugars directly, but complex sugars have to be broken into simple sugars by enzymes, which are found on your intestinal lining, before absorption becomes possible. Then the newly-minted simple sugars can be absorbed.

If complex carbs don’t get broken down (for whatever reason), then they don’t get absorbed, and they travel on down through your intestines. Then they come in contact with the bacteria in your gut. These bacteria break down the carbs for you, but they produce two major byproducts: gas (so you feel distended) and acid (which causes inflammation in your intestines). Your body responds to the inflammation by producing mucus to protect itself.

The problem is, the mucus blocks the enzymes in your intestines from coming in contact with other complex carbs you eat. So more complex carbs get turned into gas and acid, producing even more mucus.

In a nutshell: inflammation (from autoimmunity or anything else) —> mucus —> inability to break down complex carbs —> gas and acid —> more inflammation —> more mucus… and round and round we go.

So grains, even whole grains, are relatively simple carbs and can set off this process. If the gut is inflamed, as it always is in the case of autoimmunity, grains will exacerbate this process. So avoidance is best, at least until healing can occur.

My Take on Restricting Legumes

Legumes are a great source of protein, and generally very nutrient-dense. The biggest problem with them thatI can see is that 1) they contain phytic acid (an anti-nutrient of sorts: it binds other nutrients and prevents you from absorbing them; you can get around this by soaking your beans first though), and 2) they’re one of the FODMAPs, a particular type of carbohydrate very likely to cause problems for people whose guts are inflamed.

That said, I’ve yet to meet a patient who is sensitive to everything on the FODMAPs list. It’s always kind of a trial-and-error process (though I will say beans are a BIG one that tend to make most people gassy.)

I do see a decent number of patients who turn out to be sensitive to legumes on food allergy testing, though—so my best guess is, eliminating legumes on this protocol sort of follows the same logic as an allergy elimination diet. In the latter case, the idea is to restrict every common allergenic food for a period of time, and then slowly add them back one at a time. So I can see the logic if this is the reason.

My Take on Restricting Dairy (and other Gluten Cross Reactives):

I can see the logic in restricting dairy for the same reason: its allergenic potential. I wrote here on the ridiculous increase in dairy sensitivity.

Additionally, dairy can cross-react with gluten, another very common sensitivity. That means if you’re sensitive to gluten (i.e. your body is creating antibodies against it), you may end up reacting to dairy also just because there are certain segments of the dairy antigen that look very much like the gluten antigen. So even if you’re not creating antibodies against dairy itself, your body might still react as if it were.

By the way, if you’re gluten sensitive, this might also be the case with oats, millet, soy, corn, rice, yeast, rice, and potatoes. But since those are mostly grains, legumes, or nightshades anyway, it doesn’t eliminate anything new.

My Take on the Diet Overall:

I think the diet is an excellent way to cover your bases and make sure you’re not eating anything that has the potential to exacerbate gut inflammation on a number of different fronts. The foods that are recommended on this diet are very nutrient-dense, as well. For someone with autoimmunity, and especially someone who has not undergone food allergy testing to determine which foods actually do cause him or her problems, it’s a good option. My only concern is that, for patients who might say, “But what can I eat?,” it might be unnecessarily restrictive. I disagree that everyone (even everyone with autoimmunity) necessarily needs to avoid legumes, nuts, seeds, nightshades, eggs, or dairy. But if you haven’t had testing to determine whether you’re one of the people who does or not, then as with a traditional allergy elimination diet, it’s safest to just cut it out while you’re trying to heal, and reintroduce it later.

I would not recommend this protocol for someone with yeast overgrowth or SIBO, only because of the recommendation to consume large amounts of fermented foods (which can tend to exacerbate overgrowth), and the lack of restriction on fruit (ditto), while foods that should not cause any issues for these people are restricted.