5 Steps to Personalizing Your Autoimmune Paleo Protocol | Chris Kresser

5 Steps to Personalizing Your Autoimmune Paleo Protocol


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A strict Autoimmune Paleo Diet isn’t necessary for many people with an autoimmune disease. Find out why.

aip diet
Getting your autoimmune symptoms under control through the AIP diet is key to a happy, healthy life. CentralITAlliance/iStock/Thinkstock

This is a guest post by Laura Schoenfeld, a Registered Dietitian with a Masters Degree in Public Health, and staff nutritionist for ChrisKresser.com. Click here to learn more about her nutrition consulting services.

The Autoimmune Paleo Diet has been getting a lot of attention lately, even in the mainstream media. Some question if the diet is a legitimate way to manage autoimmune disease, asserting that “a lot of it doesn’t make much biological sense.”

Advocates of the diet, particularly Dr. Sarah Ballantyne (known as The Paleo Mom) and Dr. Terry Wahls, have provided heaps of evidence, both peer-reviewed and anecdotal, that the diet does indeed help those with autoimmune disease not only manage their symptoms but even begin to reverse the disease, or at least halt its progression.

As a dietitian, I’ve seen incredible results with patients who were able to successfully implement the autoimmune protocol and eliminate many of their symptoms, whether they were suffering from Hashimoto’s disease, Sjogrens, psoriasis, rheumatoid arthritis, multiple sclerosis (MS), and more. It’s amazing to see a person’s health turn around after implementing the diet change, especially when the disease they’re dealing with had been taking so much of their quality of life away from them.

While the Autoimmune Paleo Diet is a fantastic way to start seeing a vast improvement of symptoms, the major issue I see frequently is that once someone has seen success on a strict autoimmune Paleo protocol, they’re often afraid to try adding back in any foods that are eliminated from the diet.

One thing that many people don’t understand about the Autoimmune Paleo Diet is that not everyone with an autoimmune disease will need to be on this diet indefinitely.

In fact, there are few people with autoimmune diseases that would need to strictly and permanently avoid all the foods eliminated from the diet, as not everyone with autoimmunity is intolerant to all of these foods.

My goal when I work with clients is to get them on the least restrictive diet that provides the most amount of health and vitality. While those with an autoimmune disease generally have less wiggle room than the average healthy person, it’s important to remember that the Autoimmune Paleo Diet need not be followed strictly for the rest of one’s life.

A strict Autoimmune #Paleo Diet isn’t necessary for many people with an #autoimmune disease. Via @AncestralizeMe

In this article, I’ll briefly cover the five major steps to personalizing your Autoimmune Paleo Diet, in order to have the most flexible and health-promoting diet possible.

1. Start with a 30 Day Reset

In Chris Kresser’s book The Paleo Cure (formerly Your Personal Paleo Code), he suggests that everyone looking to discover their ideal diet start with a 30 day strict Paleo protocol. This means following the standard Paleo guidelines: no grains, no dairy, no legumes, no industrial seed oils, no alcohol, and so on. I believe that someone with an autoimmune disease who is currently eating a standard American diet should start with the normal Paleo 30-day reset.

There are many people with autoimmunity who will do just fine following a Paleo diet, and adding in the autoimmune diet restrictions shouldn’t be necessary in this situation. Going immediately from a standard American diet to an autoimmune protocol can be overwhelming for many people, and that’s why I generally suggest starting with the standard Paleo approach if you haven’t yet.

That said, if you have already given the standard Paleo 30 day reset a try, or perhaps you’ve been strict Paleo for many months, and your autoimmune symptoms haven’t decreased significantly, consider trying another 30 day reset. This time, I recommend adding in the standard Autoimmune Paleo Diet restrictions as well. This means additionally eliminating eggs, nightshades (e.g. potatoes, tomatoes, eggplant, peppers), nuts and seeds.

Sticking to the diet for a minimum of 30 days gives your body a chance to begin calming the autoimmune response, healing the gut lining, reducing inflammation, and repairing damaged tissues that were subject to the autoimmune attack.

I generally recommend extending the reset to a minimum of 60 days for people with severe autoimmune conditions that affect neurological function, or cause symptoms that have a noticeable impact on daily life. I’ve found that most people see enough improvement within the first 30 days that extending the reset another 30 days is no problem for them.

And remember: every time you eat a food that triggers an immune response, such as gluten, dairy, eggs, etc., your body will produce antibodies that incite an attack on your immune system for days, weeks, even months if the intake was significant enough. Committing 100% to the reset time period is crucial for a person with autoimmune disease to see the improvements they’re looking for.

It’s important to acknowledge that an Autoimmune Paleo diet is not a cure, and it may not be enough to put a disease into full remission or heal damaged tissues. Further support such as medication or targeted supplementation may be necessary to maintain the body’s optimal functioning.

That said, if you can remove the foods and toxins that are contributing to the autoimmune response and provide adequate nutrients to fuel the healing process, you can significantly reduce symptoms and even possibly put the disease into remission.

2. Optimize Your Nutrient Intake

Speaking of adequate nutrients, removing foods from your diet isn’t enough to heal from an autoimmune disease. You need to be purposeful about adding certain foods into your diet to provide the nutrients and building blocks your body needs to repair damaged organs, modulate the immune system, and heal the gut lining.

In addition to removing the common autoimmunity triggers listed above, it’s essential to add in nutrient dense foods like liver, bone broth, copious amounts of colorful vegetables, high quality meats and fats, fatty fish and shellfish, and fermented foods.

I’ve worked with patients who were following the Autoimmune Paleo restrictions beautifully, but they’d forgotten to add in some of these nutrient dense foods, which meant that their ability to heal wasn’t optimally supported.

Nutrients in liver, fatty fish and shellfish such as vitamin A and D, zinc, choline, and various B-vitamins are essential for modulating the immune response (particularly the t-regulatory cell response), supporting mitochondrial energy production, and supporting the healing of damaged tissues, especially the gut lining. (1, 2, 3, 4, 5) Liver is especially important to eat when on a strict Autoimmune Paleo (AIP) Diet, as it contains nutrients that would otherwise come from eggs, which are removed on the AIP diet.

Since the current theory of autoimmune disease is that a “leaky” and inflamed gut is required for the development of autoimmune disease, eating a diet that supports healthy gut integrity is of unmeasurable importance. (Discussing leaky gut in detail is outside the scope of this article, but if you’re looking for a program to help you through the recommended diet and supplement protocol for intestinal permeability, check out Solving Leaky Gut.)

Fermented vegetables not only provide beneficial probiotics, but also fermentable fibers that can feed the flora that are already in the gut. A healthy gut microbiome is crucial for maintaining a healthy gut lining, thanks primarily to gut bacteria’s ability to produce butyrate, which is important for t-regulatory cell production and differentiation, and can help further balance the immune system. (6)

Bone broth contains gelatin, a protein that contains the amino acids proline, glycine, and glutamine. These amino acids can help heal the gut lining, reduce inflammation, and promote healthy gut integrity. (7) Glycine in particular is known to inhibit immune activity and act as an anti-inflammatory. (8) That’s why bone broth is one of the major dietary staples of a gut healing, anti-inflammatory diet that is ideal for a person with autoimmune disease.

While many of my autoimmune patients are doing great at avoiding the foods on the AIP protocol, they still often struggle with adding in nutrient dense foods like liver, shellfish, fermented vegetables, and bone broth. These foods should be considered an integral part of an effective AIP approach, and I strongly encourage those with autoimmune diseases to make the effort to add these foods in regularly.

3. Reintroduce Foods Systematically

The benefits of reintroducing non-AIP foods are three-fold. First, you may be able to tolerate nutrient dense foods like eggs and dairy, which may improve your body’s ability to heal. Second, you’ll have a better understanding of which foods are more crucial to avoid than others, which can give you freedom in your food choices. Third, having a more broad diet can significantly improve your ability to enjoy food both at home and when out to eat, which provides important quality of life benefits.

Bonus: If you’re able to tolerate dairy, you can enjoy the nutritional benefits of grass-fed dairy. In fact, raw milk may have special benefits to those with autoimmune disease, as drinking raw milk can boost glutathione levels substantially, and glutathione is another nutrient that can modulate the immune response. (9)

Reintroducing foods is probably the most challenging part of personalizing your AIP diet. As I mentioned before, it can take hours, days, or weeks for an immune response to kick in to the point where symptoms are returning. While some people get an immediate and strong reaction to foods they eat that they have immune activity against (gluten is a big culprit here), others only have minor increases in symptoms that they may not realize are attributed to a particular food.

The best way to construct a reintroduction protocol for an autoimmune diet is to first choose which foods are the most important to you to try reintroducing, and then work systematically to bring them back into your diet. I rarely suggest trying to reintroduce gluten if you have an autoimmune disease, but other excluded foods like dairy, eggs, nightshades, and/or nuts and seeds can frequently be tolerated by those with an autoimmune disease.

Certain food groups need to be reintroduced in a particular order. The best example of this is dairy, where you start by reintroducing ghee, which contains the least amount of milk proteins, then continue with other dairy types in this order: butter, heavy cream, fermented dairy (yogurt and kefir), cheese, and fluid milk.

Other examples include eggs, which should be introduced yolk first, and nightshades, which need to be introduced one-by-one (e.g. potatoes, then tomatoes, then eggplant, and so on.) You can also reintroduce non-Paleo foods like white rice and other gluten-free grains if desired.

Chris lays out the instructions for the reintroduction phase in his book The Paleo Cure, but the most important thing to remember is to only reintroduce one food at a time, and to give yourself at least 3 solid days per reintroduction to notice any exacerbations in your symptoms.

This can be a return of your specific autoimmune symptoms such as joint pain or skin inflammation, or it may be an “unrelated” symptom like gastrointestinal distress or fatigue. If you’ve eaten the food consistently for three days and you don’t notice any negative side effects, you can generally assume the food is okay for you to eat.

4. Get Tested For Sensitivities

Sometimes the reintroduction protocol isn’t enough to discover which foods are causing you to have immune system flares. If your symptoms aren’t improving on a strict AIP diet, or if you’ve gone through the reintroduction protocol and your symptoms start to come back, you may still be eating a food that’s inciting an immune response.

In this case, getting food sensitivity testing is a good option to determine exactly which foods are the culprit. I typically see most autoimmune patients getting their testing done through Cyrex labs, which test for both IgG and IgA antibodies and can detect intolerances to a wide variety of foods.

They’ve recently released a test called Array 10 which covers a great deal of foods in both cooked and raw form, and I’d imagine this test would be beneficial to a person on the AIP diet that’s not seeing the improvements they were hoping for. Array 4 is another Cyrex test that I frequently use for patients who are unsure of whether they’re intolerant to dairy, eggs, or other foods that are commonly associated with a gluten cross-reactivity response.

It’s important to note that these tests are only accurate if you’ve eaten the food in question within the past 4-6 weeks. So if you’ve been dairy-free for 6 months, testing for a dairy sensitivity likely wouldn’t give you a positive result, even if you are truly intolerant. The testing option is more suited to people who have been eating some of the questionable foods recently and have experienced a return or exacerbation of symptoms.

If you feel that you need to get testing done to determine which foods might be an issue for you from an immunological standpoint, I strongly recommend working with a qualified practitioner who can help you navigate the testing options and interpret the results of your tests.

5. Focus on Your Lifestyle

Even though I’m a dietitian, I find that lifestyle habits other than diet often play an important role in my clients’ health outcomes. It’s always interesting to have someone come to me expecting to take on a diet change, and by the end of our first session we’ve skipped the diet and gone straight to the exercise, stress, and sleep recommendations.

Unhealthy lifestyle practices can completely undo the benefits of a healthy diet, and examining your habits is an important next step once your diet is under control.

Exercise isn’t just great for weight loss and cardiovascular health, it’s also crucial for healthy immune function. Research shows that exercise is important for T-regulatory cell production, and it can also reduce inflammation in people with autoimmune disease. (10, 11, 12, 13)

Daily exercise at a low to moderate intensity is what I’d typically recommend for people with autoimmune disease. This means avoiding excessive or overly intense exercise, allowing for adequate rest between workouts, aiming for daily low intensity movement, and limiting sedentary behavior.

As Chris explains in The Paleo Cure, chronic stress has been shown to reduce gut barrier integrity (remember the leaky gut connection?) and can trigger or worsen autoimmune disorders including multiple sclerosis, Crohn’s disease, psoriasis, and rheumatoid arthritis.

One study even found that chronic psychological stress is associated with the body losing its ability to regulate the inflammatory response. (14) The researchers even theorize that the stress connection may explain why women have a higher prevalence of autoimmune disease than men do.

I completely agree with Chris when he says:

If you’re not doing some form of regular stress management, you will sabotage all of your best efforts with diet, exercise, and supplements. 

Minimizing stress is a non-negotiable for my autoimmune clients. There are dozens of different ways you can manage stress, from yoga, to meditation, to planned social occasions with loved ones. Petting a dog, getting a hug from a significant other, or a monthly massage can all be stress relieving activities as well.

In the 14Four program, we’ve compiled a list of resources for managing stress appropriately, so check out that program if you need some assistance finding a stress management practice that works for you.

Sleep is another non-negotiable factor in my clients’ autoimmunity management plans. Chronically poor sleep is not only a source of stress, but also a source of inflammation. (15) When circadian rhythms get misaligned from weeks or months of inadequate sleep, inflammatory immune cells are produced excessively, leading to an increase in “friendly fire” against the body’s own tissues.

If you’re concerned about your sleep, check out the recommendations we provide in the 14Four program, and read Sarah Ballantyne’s excellent post on the role of circadian rhythms in regulating hormone cycles and how to get your rhythms back on track.

Sunshine is the best source of vitamin D, and good vitamin D levels have been shown to directly influence the activity of the immune system. In fact, not only has vitamin D deficiency been connected with a higher risk of developing autoimmune disease, but it also is used as a treatment for reducing the symptoms of autoimmune disease. (16, 17, 18, 19)

So don’t be afraid of the sun, particularly if you live far from the equator and/or have darker skin! And if regular sun exposure isn’t an option, you may benefit from supplementation. (Work with a professional to determine your optimal dose.)

Finally, avoiding toxins in everyday life can reduce the burden on your immune system. As an example, one study in mice showed an increased risk of developing autoimmune disease when exposed to pthalates. (20) Phthalates are relatively common chemical “plasticizers” that are found in everything from detergents, building materials, plastic food and beverage containers, and cosmetics.

You can minimize your exposure to chemical toxins by using natural products for cleaning your house and laundry, drinking out of glass bottles instead of plastics, and minimizing your use of industrial cosmetics. A great resource for DIY cosmetics is Liz Wolfe’s Skintervention Guide, and there are dozens of blog articles about how to clean without using toxic chemicals.

Get Help When You Need It!

By following these 5 tips for personalizing your autoimmune paleo protocol, I believe the majority of people with an autoimmune disease will see significant improvements in their symptoms.

That said, there are those who will need additional tweaks, deeper testing, and personalized changes to their diet, supplement, and lifestyle plan before they see the improvements they’re looking for.

This is especially true for people with severe gut issues, longterm neurological involvement, or compounding issues like surgical intervention or pharmaceutical dependency.

For those who need in depth testing and/or pharmaceutical intervention, I strongly recommend finding a qualified integrative doctor or naturopathic physician to work with.

And for those who may simply need more advice about how to tweak their diet, supplements, and lifestyle to optimize their results on the Autoimmune Paleo protocol, I’d be happy to help guide you in the right direction.

Some people with autoimmune disease need to follow a strict AIP diet—but for many with an autoimmune condition, that’s not necessary. They may find, while working with a dietitian or nutritionist, that they’re able to tolerate some foods, while others exacerbate their condition.

Understanding which foods help and which ones harm is just one step in the healing process. The next step? Working with a health coach who is able to help their clients implement the changes a practitioner recommends.

Health coaches are experts at offering support and empowering people to make sometimes difficult changes. Those changes could include letting go of some well-loved foods or adopting different daily habits that will better support immune health.

The ADAPT Health Coach Training Program teaches coaches the skills they need to support their clients as they make those changes happen. We also delve into core concepts of Functional Health, including the diet variations like AIP.

Health coaches are an important part of any collaborative healthcare team—which is one of the reasons why the career is continuing to grow. Learn more about what health coaches do and find out whether this could be the right career path for you with the ADAPT Health Coach Training Program.

About Laura: Laura uses her knowledge of traditional and biologically appropriate diets to improve her clients’ health. Growing up with a family that practices Weston A. Price principles of nutrition, she understands the foods and cooking practices that make up a nutrient dense diet.

With her strong educational background in biochemistry, clinical nutrition, and research translation, she blends current scientific evidence with traditional food practices to help her clients determine their ideal diet.

You can find her at AncestralizeMe.com, on Facebook, and Twitter!


Join the conversation

  1. Anyone have severe stomach pains and diarrhea?? I am in week 3 of AIP and cannot get rid of the severe stomach pains unless I just do not eat. Every time I eat, it causes the pain and diarrhea. I am mostly eating grass-fed beef and lots of veggies. Because of the stomach pain, I have been eating bananas instead. Bananas are the only thing that do not cause the pain. My doctor said to add in more fermented foods which I have added. I added kombucha and Gut Shot to my diet for the last 24 hours and still have not seen improvements in the stomach pain. Any suggestions? Did anyone else experience this?

    • Is it possible you are sensitive to beef? Maybe try chicken or fish and see if that helps. The other obvious thing I can think of is that maybe you are eating too many raw veggies and should try just cooked ones for awhile. I am by no means an expert, but those are the two things that jumped out at me. I would keep up with the fermented foods as long as they aren’t causing you pain, but I have found that I can no longer tolerate fermented foods, so went to a high quality probiotic in pill form instead for now.

  2. Hi, My husband is coeliac. he was so ill about three years ago, losing loads of weight and having exhaustion to the point he had a long time off work. he obviously gave up all gluten and went on a vegan diet of quinoa, rice, millet, mung beans and veg. He has recovered fairly well but still gets exhausted sometimes, tired a lot and bloated. So we decided to try the AIP. This morning he had his first bone broth and an hour later, he crashed. He suddenly became exhausted and had diarrhoea. Not sure whether this is normal or whether to continue? Please, any advice would be appreciated. Many thanks

  3. I am just finishing up my 30 days on the AIP diet. I’m not sure whether to keep on with it or start reintroducing things.
    I started the diet because I have lichen planus everywhere, and it does seem less active and is diminishing somewhat.
    One thing I have noticed is that I don’t have a lot of extra energy to burn. It seems like I run out of steam in my body if I am physically active for over an hour (just walked around at a trade show, for ex., and my energy got low quickly). I don’t really like that as a side effect.
    Anyone with the same issues or with lichen planus on how long you proceeded with the diet?

  4. Great article! One exception to the rule would be for people with histamine intolerance or mast cell activation disease. Fermented food and bone broth can cause major reactions. I was confused as to why my symptoms got worse on Aip but after making it low histamine I improved a lot.

    • Besides eliminating fermented foods, what else did you eliminate? I feel like between aip and histamine reduction, there will be nothing left to eat .

  5. I have been diagnosed with Grave’s Disease, but I have very few symptoms — the only symptoms I have had are the elevated antibodies, lumps visible only by an ultrasound, and a TSH that indicates hyperthyroidism. I do not have a racing heart, nor do I have bulging eyes — which seem like the most obvious external type of symptoms of Grave’s.

    My next blood test and visit to the endocrinologist is scheduled for 3 months from now. So if I use an AIP diet for 30 days, or even 60 days, and then start reintroducing foods — one every three days, what immune symptoms should I expect to see?

    Possibly I should follow an AIP diet simply to help my thyroid. How will I discern which foods contribute to the immune response that has led to the Grave’s Disease and lumps?

    I have always had hay fever-type allergies, and very occasionally eczema — but both are so minor that I wouldn’t consider them related to the Grave’s Disease or thyroid at all. Or even if they are related, my symptoms are so so minor that if I discerned a food allergy after reintroducing a food because of a topical skin reaction, for example, I would still need a TSH, T3, T4 and antibodies testing to see the impact the AIP diet produced a change in my Grave’s symptoms. So the reintroduction of foods after the diet seems almost like it would not really help me.

    Admin, what do you recommend? Thank you.

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