Episode 118 Transcript – Autoimmune Protocol Diet


Hello and welcome to the Ideal Nutrition Podcast. My name is Aidan Muir and I am here with my co -host Leah Higl and this is episode 118 where we’re going to be talking about the autoimmune protocol diet. And the reason we’re going to be talking about this is because a listener asked if we could talk about, and she asked very nicely. She said something along the lines of how she has an autoimmune condition and that people who promote the diet sound very convincing, but she was a little bit skeptical and wanted to know more.

And I think it is a pretty nuanced topic because when you do hear people talk about it, they can make relatively convincing arguments for it. And I guess we’ll go a little bit through the pros, cons, and what we think of it.


So starting with the theory behind this kind of diet and also talking a little bit about what autoimmune conditions are. So an autoimmune condition is where the body mistakenly attacks its own tissues which can lead to a whole host of issues and damage to the body. But the autoimmune conditions, it’s quite a broad range of conditions, but it does include things like inflammatory bowel disease, Hashimoto’s, lupus, and things like rheumatoid arthritis. They’re all individual conditions with different managements.

The information in this podcast is going to be broad because the particular protocol of this diet, I mean this diet in general is meant to be for all autoimmune conditions. And it is designed to reduce inflammation in the gut, which is then said to have an onflowing effect of healing the immune system and the gut lining. It’s also meant to improve the gut microbiome too. So those are kind of the proposed mechanisms. And a lot of this is rooted in the theory around leaky gut.So we’ll talk about what that is as well a little bit further in this podcast episode, but this diet is really linked to leaky gut and kind of that whole world.


So it is a bit of an extension of the Paleo diet, but a little bit more rigid than the standard Paleo diet. It is like a Paleo diet crossed with an elimination style diet. So like most elimination diets, it goes in the process of elimination, reintroduction, and then a maintenance slash personalization phase.

One difference with this type of elimination style diet versus others is that let’s say with IBS, if we did the low FODMAP elimination diet, we can often get, not always, but we can often get people to a point where they have pretty much no symptoms. And then when we reintroduce foods, we identify what causes symptoms quite clearly with a quite high level of conviction that that food has caused it. It’s the same kind of logic here.

But even a lot of the people promoting this are quite transparent in saying that like, this won’t always solve your symptoms completely. A lot of times it’s just aimed at a significant improvement. So that’s also how they go about this whole elimination reintroduction where you reintroduce foods one at a time and you see what identifies triggers and you can kind of figure out what could be causing symptoms for you personally is the logic behind this. And they also say, once again, from this kind of transparent way of thinking, is if you don’t see symptom improvement within two to three weeks of the elimination phase, the diet didn’t make a difference and it’s fine to stop.

And I think that’s a pretty logical way of looking at it as well for any form of elimination style diet.And another thing I should be clear on is there’s no specific autoimmune protocol diet in that there’s multiple variations of the diet because it depends on who is talking about the diet, what their personal beliefs are, what the diet should look like and everything like that. But there are a few common themes.

And one of those common themes is that it is a very nutrient dense diet, which is a huge advantage and is something that we’ll come back to. In terms of the specific foods, hard to do this over podcast. So I’ll talk a little bit about it, but we have included a list in the show notes if anyone is interested. Rather than going so much through the foods that you can eat, although that’s obviously something that the people from the other side will spend a bit of time focusing on, I’m going to talk about what it is that you need to avoid on the elimination phase of this diet.

So you need to avoid all grains, eggs, legumes, all nuts and seeds and seed oils as well. Nightshade vegetables you need to avoid as well. All dairy products and spices that are derived from seeds or derived from nightshades as well. And you also need to avoid most artificial sweeteners, most added sweeteners in general, most food additives and also alcohol and coffee as well. So it’s quite a long list of things to avoid during the elimination phase.


Before jumping into the research, we’re going to swing back around to leaky gut and its link with this diet protocol. So let’s do a little bit of a summary of leaky gut. Now this can be a complicated topic because leaky gut as a standalone diagnosis is not recognized by the medical field, but it is recognized by more natural medicine professionals, so things like naturopaths and homeopaths.

But regardless of whether leaky gut can be a diagnosed condition, whether it’s real, we do know that intestinal hyperpermeability is a real thing. So let’s talk about what that is and then how that relates to the autoimmune protocol diet. So the digestive tract is where obviously where food is broken down and nutrients are absorbed into the body’s circulatory system.

The human digestive system is really tightly regulated in regards to what can actually pass through into the blood. There are small gaps in the intestinal walls called tight junctions and that allows water and certain nutrients to pass through, obviously so it can be absorbed into the bloodstream. But larger particles like toxins and bacteria and other things are usually prevented from passing through into the bloodstream.

But when intestinal hyperpermeability is present, these tight junctions are not as tightly regulated. So these larger particles can then pass through into the bloodstream. And that is what is quote unquote, leaky gut. So these terms can kind of be used interchangeably. And we do know intestinal hyperpermeability is a thing that happens. It is a physiological thing that does occur.

What we’re not sure about and what is the big question mark is like, is leaky gut the cause of certain conditions or is it just a kind of a symptom of certain conditions? So how it links to the autoimmune protocol diet is that basically certain dietary things have been linked to leaky gut or intestinal hyperpermeability and the thought is okay if we can then heal leaky gut through what you consume from a diet perspective then it might heal the autoimmune conditions that it’s potentially causing. So that’s kind of the link there.


So there’s no research directly on the intestinal permeability side of things with the autoimmune protocol to the best of my knowledge, but we’re going to explore the general research that exists on the AIP diet. So we only have three relevant studies to the best of my knowledge that are published as of right now in 2023. The diet has been popularized since around 2011 slash 2012.

Paleo has been popular since around 2002. So that adds a bit of context in regards to research we have around that. I like to add context on that for two reasons. One, 2011 -2012 means it hasn’t been around for like ever, but it has been around long enough that if something’s like super, super effective, often we’d be seeing quite a lot of studies on that, which gives away a little bit of stuff. But I’m gonna go through each study individually.

So the first study was in 2017 and it was titled ‘efficacy of the autoimmune protocol diet for inflammatory bowel disease’. It was an 11 week study in 15 people with inflammatory bowel disease. Some of them had Crohn’s, some of them had ulcerative colitis, so it wasn’t just unique to either of them specifically. They followed the autoimmune protocol diet. The participants all reported experiencing significantly fewer inflammatory bowel disease related symptoms by the end of the study. However, there were no significant changes in markers of inflammation that were observed.

Obviously one of the arguments for this diet has been a reduction in inflammation, but there was no change in markers that were observed. A few other interesting points, of those 15 people, three had vitamin D deficiency and six had iron deficiency at the start of the study. Those nutrients were supplemented as well, so that was an additional kind of benefit that they were given. Participants were also given two books.

One was called The Paleo Approach by Dr. Sarah Ballantyne. I spent a lot of time on YouTube watching her videos just to get my, like just to get both sides of this kind of like discussion as well. So she’s one of the leading kind of proponents of this. The other one was called the autoimmune wellness handbook by Mickey Trescot and clinical remission was achieved in six weeks, which was the elimination phase in 11 of the 15 participants. That’s 73%. That’s huge.

For context, there is a diet called the Crohn’s disease exclusion diet, which is practiced in hospitals where they feed people nasogastric -ly and about 80 % of people go into remission on that diet. So like that’s the nasogastric feeding kind of tube where all the food is provided. They have no choice apart from giving the diet they’re given. Whereas to the best of my knowledge in this study, they were just eating as free living individuals. So like 73 % remission rates, pretty solid. And once again, key point, all participants experienced improvements in their symptoms, even if remission wasn’t achieved in 100 % of people.

The second study was basically just a repeat of that study. So it was done in 2019, same thing on inflammatory bowel disease. Another 15 people did the same thing. Once again, they all reported significant improvements in things like bowel frequency, stress, and the ability to perform leisure or sporting activities as early as three weeks into the study. So there were no improvements pretty quickly. Won’t spend too much time on that because that’s pretty much the same as the first one, but it’s just cool to have a repeat of that study.

And then the third one, it was on a different autoimmune condition. So this third one was on Hashimoto’s, so a thyroid condition and it was done in 2019 as well. They had 16 women with Hashimoto’s follow the autoimmune protocol for 10 weeks. By the end of the study, inflammation as measured by CRP actually had decreased by about 29 % and disease related symptoms had decreased by 68%, which once again is pretty huge. Participants reported significant improvements in quality of life and another key thing was that like no changes in measures of thyroid function were observed though. So measures of T3, T4 and thyroid antibodies remained unchanged.

So similarly to the inflammatory bowel disease where like no inflammation changes are measured there, in this case, some key markers that we would kind of want to be seeing changing remained unchanged, which gives you a bit of a mixed bag where it’s like, we care about quality of life and symptoms and outcomes quite highly. And these were things that were improved. But some of the key kind of things that you would kind of expect to change alongside that didn’t change alongside that, which makes these studies interesting.


Yeah, it definitely makes it interesting that we’re seeing changes in like symptoms and quality of life, but not necessarily the the numbers on blood tests and things like that. So very interesting. So moving on, let’s talk about reasons not to do the autoimmune protocol diet. It all sounds positive, but I think we’ll approach it in a positive way. Like obviously there’s not a ton of research. What we do have seems pretty positive. So we’ll run through and do a bit of a balanced reasons not to do it, reasons to do it and kind of do a bit of a summary from there.

So reasons not to go through with this diet, starting with the obvious, it’s restrictive. Like any kind of elimination diet, you’re obviously having to cut out a lot of different kinds of foods, which could be a problem in social situations. It could just be annoying. Maybe it’s not worth it for you. And then looking at more serious stuff, if there is a case of disordered eating or background of an eating disorder, then perhaps this is not a route you want to go down either. So that’s the obvious stuff.

Some less obvious stuff, although it is a nutrient -dense diet the limited food choices in combination with maybe like limited food preferences. Maybe you don’t like a lot of what is left on the list. Maybe it’s cutting a lot of things out that you would usually enjoy. Maybe that’s going to result in some issues with getting insufficient calories, macronutrients and micronutrients.


I’ll also jump in on that. Like watching the like Dr. Sarah Ballentine YouTube videos, she was talking very positively about the benefits of eating awful like organ meats, particularly liver. And she was kind of like, I often get the question, what if you don’t like to eat liver? And she’s like, but you’ve still got to do it. Like, I know it sucks, but like, you’ve got to get it in. You’ve got to get in three to three to four times per week on this diet. Yeah. And just kind of like left it there. And like, I get what she’s saying, but then it is coming back to being like, there is far see food preferences, like some people as hard to get to eat vegetables to start off a little.


100%. I feel like asking people to eat those kinds of like organ meats and whatnot is, it’s a hard sell because most people are not wanting to try that. But that is part of what makes this dietary protocol so nutrient dense. So you’d be missing out on potentially a huge factor. So yeah, that’s definitely something to consider.

Something else to think about is that we also see benefits from other dietary changes that may not be as restrictive or as intense as this whole autoimmune protocol diet. So a good example of this is a 2020 systematic review on nutrition for lupus specifically. And that found that a low calorie, low protein diet, high in fiber, omega -3, omega -6, polyunsaturated fats, as well as vitamins A, B, C, D, and E as well as some minerals, calcium, zinc, selenium, iron, copper, and polyphenols. So it was very nutrient rich diet, just following a completely different, I guess, protocol to the diet we’re talking about. But this also improved symptoms and quality of life for lupus patients.

So it’s like, there are other dietary approaches that perhaps are looking more at what we can add to our diet, more so than maybe what we have to restrict from our diet that could also have a great benefit so it’s not like there is this guarantee that the autoimmune protocol diet is like that’s the ‘one and done’ that’s the one stop shop for autoimmune conditions because there is limited research even though so much of it is positive at this point.

There’s also the point that when we are doing elimination style diets if someone was to find a huge benefit from an elimination diet are they then going to be reluctant to reintroduce stuff in the future. Is someone potentially going to do the autoimmune protocol diet go? Well, I feel great This is improved my quality of life and then just stay on that forever and how would that then go on to affect potentially long -term health?


Yeah everything else they’re cutting out and like that seems like a little bit of a weird concern But like we do see that all the time like I see on social media. I say when clients like slightly less restricted but like the low FODMAP diet. I Isee clients who’ve been like you have in life about for a year and they’re still getting symptoms as well. It’s just like it hasn’t solved their symptoms. They’re still doing it. They’re still very restricted and they haven’t tried reintroducing stuff, but it’s partly because if they went to reintroduce stuff, they couldn’t really tell because they’re also getting symptoms already.


Yes, exactly. It can be a bit of a rabbit hole on its own, that particular concern, but it is a concern that we, you know, it’s worth kind of adding on to this list as well.

We haven’t touched on the flaws of the paleo diet specifically or in general, because that’s too big of a podcast to do, but that’s also something to consider is like, there are many flaws to the paleo diet, particularly in terms of it’s like logic, like, does it really check out enough for us in regards to proposed mechanisms to be worth doing at this point?


Yeah, like touching on certain things, like a lot of the logic in this is based around reducing inflammation and also leaky gut stuff. And, how many certain foods were excluded that may or may not have played a role in the information to start off with. There’s a lot of things to think about with that. Like there could be aspects that could be refined, et cetera.


It’s like, how did they come up with this list specifically? Like with other elimination style diets, you have FODMAPs. Well, all the foods that you’re eliminating are high FODMAP. Yeah. Food chemical, all the foods, they all have like a certain, you know, but it’s like this list of foods, like how are we actually coming up with it?


Yeah, so the opposite perspective we’re going to look at is looking at reasons to try the AIP. So basically, the first thing that I think is an interesting way of me thinking about it is every time I open any form of autoimmune protocol diet study, like any research on it, knowing that there’s also some unpublished research that I’ve kind of also read and had the results, etc. but hasn’t been published. There’s sort of been published as a few other ones just floating around that haven’t been published. But every time I’ve opened a new one as I’ve gone through researching this, I expect participants to see improvements. And that’s just an interesting thought, just being like, okay, this is consistent enough that every time I open a study, I assume people are gonna get some form of improvement. Kind of makes sense to be like, okay, well, that’s one thing that could make it a little bit compelling to try.

Another thing is that trial and error is often involved in autoimmune conditions anyway. This is just one way of doing it in a little bit more of a systematic way, where it’s like you do the elimination for like up to six weeks or whatever, and then you start the reintroduction process outside of the restriction aspect, although we talked through a bunch of reasons that are downsides, there is also minimal downside to trying it for a short period of time, like outside of the restriction aspect.

Another very positive thing is it is extremely nutrient dense, which we’ve touched on. But going back to Dr. Sarah Ballentine, watched too many YouTube videos first, so I’m just going to invite some of her stuff. But like, she talks about it in like her writing and her presentations that in autoimmune conditions, the body is starved for nutrients emphasis on the word starved. I personally wouldn’t use that wording.

But something we do see in a lot of research on autoimmune conditions is that it is quite common for there to be certain micronutrient deficiencies. And that potentially could increase the risk of these autoimmune conditions and or increase the severity of them as well. I think addressing them is a good thing to do regardless. And you could do that with supplements, et cetera. But following a nutrient rich diet is a great place to start since it will indirectly address a lot of stuff without you even needing to identify the individual deficiency. So this is one way of doing that. And using the organ meats as an example, like they are super high in things like vitamin and a few other things that it’s harder to get as much of in certain ways. So it’s like, that’s one kind of benefit of this type of approach.


As a bit of a summary, so like from one perspective, the research we have so far is super promising, which we have stated, particularly since pretty much everybody in these studies have noticed improvements. So maybe they didn’t get a full resolution of symptoms, but most people, if not everyone, noticed some improvement.

It is also not a forever diet. So it’s not something you need to stay on forever. You trial it. If it works, great. You reintroduce. You see what is triggering you specifically. You reintroduce everything else that you were previously restricting. So there’s not much lost in all of this. Like I said, not something you have to follow forever.

But from the other perspective, we do have minimal research. So what we have is positive, but there’s still not that many studies. The studies are still quite small in regards to number of participants. So that’s something to consider as well. And these studies are also not exactly placebo controlled. So they were receiving like books and stuff that were specific to the autoimmune protocol diet and were pro that particular diet. So that could have been playing a role somewhat in their resolution or improvement of symptoms.


Yeah, and at least even like reporting of symptoms. Like if you’ve just spent 11 weeks reading about the benefits of the diet that you’re on and then you get to end of it and you get asked your symptoms in relation to what the diet was supposed to help, like it is likely you report better symptoms as well. Only a small factor, but it is a factor that I think is relevant versus a lot of other dietary approaches where we have control groups and everything like that that we’re compared to.

Some other personal opinion stuff just from me is this has been an option since 2011, 2012 as I touched on. And I do lean into that kind of concept of being like, if there hasn’t been heaps of research published on something that’s been around for over 10 years or around 10 years, actually no, it is over 10 years. It does make you think like, why? Why is not there not being more effort put into place here?

Using a condition that wasn’t studied as an example, rheumatoid arthritis. As of 2023, there doesn’t seem to be any kind of like universal solution for rheumatoid arthritis. There’s a lot of things that people can do that can improve symptoms a little bit. There’s a bunch of stuff like that. But there’s not really anything where it’s like, hey, give me 100 people with rheumatoid arthritis, give them this dietary approach, they should all see massive improvements. Like there’s nothing like that. And a lot of people with rheumatoid arthritis will want something like that.

And it makes you think, why isn’t research being done like that? If it seemed like it was consistently going to be providing good outcomes, you’d think more research would be done. And even if I’m wrong with my interpretation there about the research side of things, if there was consistently seeing these huge improvements, you’d still become mainstream anyway, because people talk, like people talk being like, I did this process, this gave me huge improvement. If it’s consistently doing that for a large percentage of people, you would expect that. Apart from the only downside of me saying that is like, it’s a hard thing to do this diet. It’s quite a restrictive diet.

And then the final thing that I wanted to come back to is that whole concept of the lack of change with certain markers that are important. For example, in inflammatory bowel disease, no change in inflammation is kind of a key marker. So I have mixed feelings on it in terms of being like kind of restrictive, plenty of downsides we talked about. Don’t want to ignore all the improvements that have been seen over those three studies that have been talked about as well, but then also want to acknowledge that they could also be achieved in many other ways. For example, as you talked about with those nutrient rich diets in general, showing improvements too, that should be factored in as well.


This has been episode 119 of the Ideal Nutrition Podcast. If you haven’t yet left a rating or review, it would be so greatly appreciated for you to do so. But otherwise, thanks for tuning in.