Why I Don’t Believe in the Autoimmune Protocol (AIP)

Why I Don’t Believe in the Autoimmune Protocol (AIP)

The rise of autoimmune disorders these days (there are over 100 types of known autoimmune diseases alone) also gives rise to a multitude of ‘solutions’ being offered.

Restrictive diet plans are big business these days. Keto, Whole30, Paleo, and of course, there is one for autoimmune too: the Autoimmune Protocol, also known as AIP. If you have navigated in the autoimmune world, you’ve most likely heard of it. If you haven’t, you probably would’ve heard of it too. It’s definitely made its rounds.

Why Not Autoimmune Protocol AIP Diet on Nourish Natural Wellness

Disclaimer: If you are an Autoimmune Protocol (AIP) fan or follower, or if you have experienced a positive change in your health or even recovered from one or more autoimmune diseases all due to following this diet plan, then well done, it was no easy feat. This piece contains merely my opinion and interpretation of this diet plan.

What is Autoimmune Protocol (AIP)

The Autoimmune Protocol is a restrictive diet plan where one eliminates a list of foods from their diet in an attempt to identify food allergies and food sensitivities. According to the diet, these foods to eliminate may cause inflammation in the gut. The theory is that autoimmune conditions are caused by a ‘leaky gut’, a condition where small holes in the gut cause food to leak into the body, causing the immune system to overreact and start attacking our own healthy cells.

Foods to eliminate

The diet calls for removing quite a list of foods, from grains, beans, legumes, dairy, eggs, nuts, seeds, nightshade vegetables, and food chemicals and additives.

Although I pretty much stand for eliminating food chemicals and additives even when you don’t have autoimmune or any health condition, I can’t quite wrap my mind around the rest of the foods in the ‘elimination’ list. These, to me, are perfectly good plant foods with good nutritional values.

Foods to eat

The diet also advocates eating more foods believed to be ‘nutrient-dense’, such as bone broth, good-quality meat and wild-caught fish, as well as organ meats, fermented foods and a wide variety of fruits and vegetables.

I am all for a wide variety of nutrient-dense foods, including fruit and vegetables, good quality fermented foods, and reasonable amount of foods from animal sources. My ideal ratio is 80% plant foods and 20% animal foods, some days the numbers fluctuate but we hover around there.

The claims

By eating nutrient-rich foods (except for the nutrient-rich foods to be avoided, obviously) and avoiding ‘inflammatory’ foods, the diet “aims to heal any holes in the gut”, which in turn help:

  • reset the immune system
  • prevent the autoimmune response
  • reduce symptoms of autoimmune diseases
  • prevent the occurrence of secondary autoimmune diseases [1]

How it works

One would follow the list of foods to avoid and foods to eat strictly for anywhere between a month to a year (!), a period they call the ‘elimination phase’. During this time they would take note of how they feel and if they experience any changes in their health.

After the elimination period, they are to then slowly (and systemically) reintroduce these foods back into their diet. The idea is to see if there is a reaction when the food is reintroduced. If there is a reaction, the suggestion is that the foods that are the culprits be avoided for the long term. Based on this ‘experiment’, they are to then come up with a list of foods they can and cannot eat for the long term.

To me, if at best at the end of this experiment one experiences a positive shift in their autoimmune condition, they are most likely bound to a restrictive diet for as long as one can see.

Limitations of the Autoimmune Protocol elimination diet as a way to resolve autoimmune disorders

By now it’s become clear to me what is missing from this type of restrictive diet as a way to resolve autoimmune disorders. But let me break it down further.

5 limitations of Autoimmune Protocol AIP diet on Nourish Natural Wellness

The cons

1. It is extremely hard to follow and sustain for the long run.

I don’t believe that anyone following this diet plan isn’t wishing that they have another option to get better without having to eliminate so many foods from their diet.

2. Some of the foods in the “to avoid” list are wholesome plant foods with nutrients that are supposed to be beneficial for our health.

These include plant foods that contain a variety of healthy and important nutrients, such as:

  • Beans and legumes
  • All the vegetables classified as ‘night shades’
  • Nuts and seeds
  • Eggs and dairy (in moderation)

Although the grains to be avoided may not be the highest source of nutrients, they still contain a variety of vitamins, minerals and in some cases fibre. The bottomline is, our body should not be reacting badly to these foods that the human race has survived on for millennia.

3. You are mainly left with getting your protein from animal based foods.

Plant based protein is preferably to animal sources as plant foods pack more nutrients into fewer calories, contain fibre which in turn promote a healthy gut microbiome (something that animal proteins do not have), are low in fat and cholesterol, and are less susceptible to health risks associated with meat contamination, antibiotics in meat products, and cancer-causing compounds from cooking meat at high temperatures.

4. This diet and its theory focuses on leaky gut instead of our immune system, which is the core machine that’s keeping us alive and is the force behind the autoimmune disease itself.

Our immune system works around the clock to constantly protect us from all sorts of internal and external threats. With an autoimmune diseases, there aren’t enough questions asked as to WHY they occur in the first place.

Why would our body react badly to foods that the human race has survived and thrived on for centuries and even millennia? If billions of people around the world can be perfectly healthy eating these foods, why do we get so sick from eating these wholesome plant foods? The answer is: a malfunctioning immune system. The fact that our body reacts to these foods thinking that they are enemies is the problem. Avoiding the foods merely avoids the problem. In my opinion, we should fix our immune system, not heal a leaky gut.

5. Bigger problems could arise down the road

Related to #4 above, if we don’t address the root of the problem, and merely avoid foods we believe are wreaking havoc in our bodies, bigger problems may arise.

If our body is whacky enough to react badly to perfectly healthy foods – tomatoes or eggplants for example – and you just cut these foods off your diet, what if that whacky system reacts badly to even more or different foods down the road? Are you then back to square one, doing the elimination diet all over again? This is likely as the root of the problem itself is not fixed.

The elimination period which lasts between a month to a year may sound awfully long for such an extreme diet. But just because your body doesn’t happen to be rejecting certain foods during your experimental period, doesn’t mean it won’t reject these foods down the road if it continues to be whacky.

Instead, look to restore the balance of your immune system by using foods with powerful polysaccharides and fix the root of the problem for the long run. Nutritional Immunology advocates for eating a wide variety of wholesome plant foods, including vegetables, fruit, nuts, seeds, beans and legume in addition to more potent foods like cactus, certain types of mushrooms, rose, cactus fruit, ginseng, and so on.

The pros

Some of the foods to be avoided, especially when you’re trying to recover from an autoimmune condition, make perfect sense, for example food chemicals or additives, alcohol, and too much sugar. I advocate for avoiding these foods even when you don’t have a health condition regardless, so to me this is the only bright side I can see from the Autoimmune Protocol (AIP).

I originally wrote this article for “Natural Alopecia Wellness“, a website that is dedicated to helping others resolve autoimmune-triggered hair loss condition called Alopecia Areata.


  1. All you need to know about the AIP diet
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