The Autoimmune Protocol

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TPA as a bookThe Paleo Approach is now available!   If you want the nitty gritty details (explained in an approachable way!), the diagrams and illustrations, the scientific citations, all of the information in one place, FAQ, information on supplements, help troubleshooting, practical implementation tips,  food lists, it’s all in my book:

Buy Now!

Note:  I will always keep this cliff notes version of the autoimmune protocol here for free for everyone to see.  That’s right.  I’m not holding this information hostage.  While my book goes into far more detail and explains the detailed WHYs behind these recommendations, you don’ t need to buy it to start making positive changes that can help regulate your immune system and heal your body.

Interested in learning even more about The Paleo Approach? This video from my YouTube Channel is just a quick tour (the book is so big that giving you a broad overview takes 13 minutes!) but you get to see just how comprehensive and detailed this book is.

My original research into the dietary guidelines for those with autoimmune disease started with the recommendations in The Paleo Solution, The Paleo Answer, and various podcast and YouTube interviews with Robb Wolf, Prof. Mat Lalonde and Dr. Terry Wahls (author of Food As Medicine and Minding My Mitochondria). These are all great sources for more information while you wait for my book to be released. However, as I have delved into thousands of scientific studies (1200 of which are referenced in my book) evaluating the roles of nutrients, hormones, and the bacteria in your gut in the development or prevention of autoimmune disease, I have refined these recommendations to reflect my new-found (very thorough) understanding of how the foods we eat interact with our gut barriers and influence our immune systems.

Autoimmune disease is caused by the immune system losing the ability to differentiate proteins belonging to your own body with proteins belonging to a foreign invader (like a bacteria, virus or parasite). What causes symptoms is the build up of damage to cells, tissues and/or organs in the body–damage caused by your own immune system attacking those cells. Which proteins/cells are attacked is what separates once disease from another. In Hashimoto’s Thyroiditis, the thyroid gland is attacked. In Rheumatoid Arthritis, the tissues of your joints are attacked. In psoriasis, proteins within the layers of cells that make up your skin are attacked. However, the root cause is the same.

Genetic predisposition to autoimmunity makes up about one third of your risk of developing an autoimmune disease. The other two thirds of your risk come from environmental factors, which include: diet, lifestyle, infections (both prior and persistent) exposure to toxins, hormones, weight, etc. While you cannot control your genetics or whether or not you had mono as a kid, you do have an immense amount of control over your diet and lifestyle (and the extent that these affect hormones and weight and even toxin exposure). By removing the foods that contribute to a leaky gut, gut dysbiosis (the wrong numbers, relative quantities, or types of microorganisms typically growing in the wrong locations in your gut), hormone imbalance, and that stimulate inflammation and the immune system, you can create the opportunity for your body to heal. By addressing important lifestyle factors and changing your focus to eating nutrient-dense foods that support optimal gut health (and optimal health of your gut microorganisms), that restore levels of important nutrients and provide all of the building blocks that your body needs to heal and properly regulate the immune system, that help resolve inflammation and support organ function, you create an environment in your body conducive to healing.

This is not a cure (once your body learns to attack itself, it can never un-learn this), but you can put your disease into remission, often permanently. Depending on how long you have had your disease and how aggressive it is, there may be permanent damage (which might, for example mean that you need to take organ support supplements such as thyroid hormone in the case of Hashimoto’s thyroiditis for the rest of your life), but you can stop your immune system from attacking your body and heal substantially.

This diet is appropriate for everyone with diagnosed autoimmune disorders or with suspected autoimmune diseases. It is very simply an extremely nutrient-dense diet that is devoid of foods that irritate the gut, cause gut dysbiosis and activate the immune system. You will not be missing out on any nutrients and this diet is absolutely appropriate to follow for the rest of your life. If you have a specific autoimmune disease that causes extra food sensitivities, those should be taken into account with your food choices. Because I get asked this question more than any other question: yes, this diet will help you.

One of the most important contributors to autoimmune disease is nutrient deficiency (which of course, is built right into the Standard American diet, which while being rich in energy is very poor in actual nutrition). Even if you have been following a paleo, primal, GAPS, SCD, or WAPF diet for a while, it is likely that you have not corrected nutrient deficiencies (if you had, you probably wouldn’t be reading this page).

Gut dysbiosis and a leaky gut are believed to be involved in all autoimmune diseases (and are present in every autoimmune disease which has been tested). The presence of gut dysbiosis and a leaky gut are directly related to diet and lifestyle (the foods you eat, the foods you don’t eat, how much sleep you get and how stressed you are). The diet recommendations of The Paleo Approach are all designed to help heal the gut, to restore normal/healthy gut microorganisms, to reduce inflammation and to regulate the immune system both through healing the gut, regulating hormones and addressing micronutrient deficiencies.

My understanding of autoimmune disease goes beyond diet. The Paleo Approach will go into great detail about exactly why prioritizing sleep, managing stress, protecting circadian rhythms, and incorporating plenty of mild to moderately-intense activity (and avoiding strenuous activity) into your day is also exceptionally important. In fact, if you ignore these lifestyle factors, you might completely undermine all of the efforts you are making with your diet.

The first dietary recommendation for those with autoimmune disease is to adhere to a strict paleo diet with no cheating. To be clear, this means: no grains, no legumes, no dairy, no refined sugars, no modern vegetable oils, no processed food chemicals. While other people may be able to enjoy the occasional bowl of rice or corn chips or even ice cream, if you suffer from an autoimmune condition you are not one of these people. Gluten should be banned for life. Grains and legumes should never be consumed. Dairy of any kind (even grass-fed ghee which can still have trace lactose and dairy proteins!) should be avoided initially. This may be true for the rest of your life but some people may be able to reintroduce many foods after their diseases are in remission.

In addition, if you have an autoimmune condition, you should completely avoid:

There are a variety of reasons these are omitted, including: causing gut irritation, causing gut dysbiosis (overgrowths are most common), acting as carrier molecules across the gut barrier, acting as adjuvants (stimulating the immune system), increasing gut permeability, causing inflammation. In addition, you should ensure that your blood sugar levels are well managed (this should happen naturally but for those with a history of diabetes, obesity, and/or metabolic syndrome, using a glucometer may be helpful). This does not mean low carb. It just means not high carb.

There is also some evidence that hormonal birth control can contribute to hunger and digestive hormone dysregulation, leading to inflammation and immune activation.

Perhaps even more importantly than removing foods that negatively impact gut health or stimulate the immune system, is eating a nutrient-dense diet. Micronutrient deficiencies are the strongest diet-related factors contributing to increased risk of autoimmune disease. If you have autoimmune disease, it is highly likely that you are deficient in one or more of: fat soluble vitamins (A,D,E,K), several minerals (zinc, iron, copper, magnesium, selenium, iodine, etc.), B-vitamins, vitamin C, antioxidants and other non-vitamin nutrients (like CoQ10), omega-3 fatty acid (in relation to omega-6 fatty acid intake), certain amino acids (like glycine), and fiber.

So, just as some foods should be eliminated, there is also a focus on eating more of the following:

  • organ meat and offal (aim for 5 times per week, the more the better)–read more here.
  • fish and shellfish (wild is best, but farmed is fine) (aim for at least 3 times per week, the more the better)–read more here and here.
  • vegetables of all kinds, as much variety as possible and the whole rainbow, aim for 8-14 cups per day
    • Green vegetables
    • Colorful vegetables and fruit (red, purple, blue, yellow, orange, white)
    • Cruciferous vegetables (broccoli, cabbage, kale, turnips, arugula, cauliflower, brussels sprouts, watercress, mustard greens, etc.)
    • Sea vegetables (excluding algae like chlorella and spirulina which are immune stimulators)
  • quality meats (grass-fed, pasture-raised, wild as much as possible) (poultry in moderation due to high omega-6 content unless you are eating a ton of fish)
  • quality fats (pasture-raised/grass-fed animal fats [rendered or as part of your meat], fatty fish, olive, avocado, coconut, palm [not palm kernel])
  • fruit (keeping fructose intake between 10g and 20 g daily)
  • probiotic foods (fermented vegetables or fruit, kombucha, water kefir, coconut milk kefir, coconut milk yogurt, supplements)–read about them here and here.
  • glycine-rich foods (anything with connective tissue, joints or skin, organ meat, and bone broth)

You can also improve your intake of important trace minerals by switching to Himalayan Pink Salt or “dirty” sea salt. Other tips like eating locally-grown organic produce can make a big difference (both in terms of micronutrients and in terms of probiotics). It is also very helpful to drink plenty of water between meals and to make sure you are consuming enough food. The body is not very efficient at healing itself when you are running a caloric deficit (you shouldn’t have to gain weight to heal, but losing weight may be a competing goal for now). If you are underweight or worried about losing weight, see this post.

Fruits and vegetables may be consumed raw or cooked. I recommend eating the rainbow and including something green with every meal (or at least most of them) and as much variety as possible. The only fruits or vegetables that are restricted on The Paleo Approach are nightshades and legumes. Dried fruit are high sugar and should be reserved for occasional treats due to their potential impact on blood sugar. All other fruits and vegetables are low or moderate glycemic load (which is more relevant than glycemic index in terms of impact on blood sugar) and the vast majority of people will be able to sufficiently regulate blood sugar levels without limiting or counting fruits or vegetables at all. In fact, eating a large amount of vegetables is really important and I think that there are so many fears about which vegetables might be bad (starchy vegetables for SIBO, FODMAPs, Salicylates, histamines (teaser excerpt from The Paleo Approach on this coming soon), goitrogens, insoluble fiber, high sugar from fruit, etc.) that people under-eat fruits and vegetables to the detriment of their healing. While some of these are certainly worthy areas to explore should you not experience dramatic improvement in 3-4 months, unless you have diagnosed fructose malabsorption or diagnosed histamine or salicylate sensitivity, that isn’t where you should start. Don’t like vegetables? I don’t care. Eat them. Eat liver, fish and oysters too.

Some quick myth-busting and FAQ:

  • Starchy Vegetables (GAPS, SCD): Avoiding starchy vegetables for SIBO has not been validated in the scientific literature (but eating low FODMAP has been proven very effective for people with IBS, IBD and SIBO). Many people do anecdotally find symptom relief from starving overgrowths with these very low carb approaches, but the low carbohydrate/fiber intake can be stressful on the thyroid and cause dysregulated cortisol (and both of those are bad!). The two diet factors that have been shown in the scientific literature to have the most dramatic corrective impact on gut microorganims is high omega-3 fatty acid intake (lots of fish!) and high fiber intake (from vegetables and fruit), both soluble and insoluble. If you do have confirmed SIBO or strong gastrointestinal symptoms, you may want to combine the autoimmune protocol with a low FODMAP approach or you may wish to save low FODMAP for troubleshooting a month or two down the road.
  • Insoluble fiber: While insoluble fiber gets a bad reputation as being an “irritating” fiber, recent studies actually show that higher insoluble fiber intake speeds healing in models of colitis and diverticulitis. Also, the higher the intake of insoluble fiber, the lower the chances someone will have high c-reactive protein (implying that it reduces or prevents inflammation). Soluble fiber reduces the chance of having high c-reactive protein too, but not as much as insoluble fiber. Insoluble fiber also reduces risk of cancer and cardiovascular disease. I can’t find a single scientific journal article that actually shows that insoluble fiber irritates the gut and I have a feeling this is myth. Instead, I can find evidence that it reduces bile acid loss (which ultimately improves digestion), is an essential signal for ghrelin suppression after meals (which has a ton of different important effects in the body), that it improves insulin sensitivity, and helps to remove toxins from the body. I can’t find a single reason why insoluble fiber should be limited. If you have intact pieces of high insoluble fiber vegetables in your stool, add digestive support supplements (especially plant enzymes) and try limiting yourself to cooked vegetables until your digestion improves. For more information, see Part 1, Part 2, Part 3, Part 4 and Part 5 of my Fiber Manifesto series.
  • Goitrogenic vegetables for thyroid disorders: Again, there is no scientific evidence for their exclusion even for those with thyroid disorders. I explain in detail in this post.
  • Fruit: Many people avoid fruit because it is high in sugar. If you have FODMAP-intolerance, you will want to avoid high fructose fruits and everyone will want to keep their fructose intake below 20g per day, but fruit in moderation is endorsed and is actually a great source of vitamins, minerals, fiber and antioxidants. Depending on which fruit you choose, and how you define a serving, you can typically enjoy 2-5 servings of fruit per day and stay below 20g of fructose.
  • Omega-3 intake is very important: Aim for between 1:1 and 1:3 ratio of omega-3 fatty acids to omega-6 fatty acids. If you eat grass-fed, pasture-raised meat, not too much poultry, and some fish, this will be natural. If you eat more conventional meat or more frequent servings of poultry, you will need to increase your intake of oily cold-water fish (like salmon, mackerel, sardines, herring, kipper, anchovies, trout, fresh tuna, and carp). Rendered animal fats used for cooking should always come from grass-fed or pasture-raised animals. Omega-3 fatty acid intake is one of the most important factors for correcting gut dysbiosis. It is better to get your omega-3 fats from fresh fish rather than fish oil. Plants-based omega-3s are predominantly ALA, which is not as usable by your body as the long chain DHA and EPA in fish and pasture-raised/grass-fed meat. Increasing omega-3 fatty acid intake has been shown to dramatically reduce the need for NSAIDs in patients with Rheumatoid Arthritis.
  • Protein is important: You can heal your body by limiting your animal-based foods to fish and shellfish, but you need protein. The protein in fish and shellfish is more digestible than meat (and meat protein is more digestible than any protein from plants), which may be relevant for those with severely damaged guts.
  • Vegetables are important: don’t skimp on the vegetables. If you are a person who has a very hard time eating large servings of vegetables, smoothies or vegetable juices might be consumed in moderation as part of a meal (and not as a meal replacement because chewing is an important signal for digestion). If you have trouble digesting large amounts of vegetables (if you have any gastrointestinal symptoms or can identify intact vegetable particles in your stool), try taking digestive support supplements with your meals and limiting yourself to cooked vegetables initially (plant enzymes are especially helpful for breaking down fiber).
  • Gray Areas: egg yolks, legumes with edible pods (such as green beans and snow peas), walnut oil, macadamia nut oil, grass-fed ghee, and gluten-free alcohol when used in cooking are gray areas. I suggest omitting them in the beginning, but can typically be reintroduced much earlier than other foods. Whole coconut products (coconut butter, coconut cream concentrate, creamed coconut, coconut flakes, coconut chips, fresh coconut) should be consumed in moderation (due to being very high in inulin fiber and moderately high in phytic acid). Coconut milk and coconut cream (not to be confused with creamed coconut or coconut cream concentrate) should be guar-gum free and limited to 1 cup per day. Coconut oil is fine if well-tolerated.
  • FAQ Foods:
    • carob, rooibos tea, black and green tea in moderation, DGL, apple cider vinegar, wine vinegar, balsamic vinegar, coconut water vinegar, coconut water in moderation, vanilla extract (if cooked), pomegranate molasses in moderation, maple syrup and maple sugar very occasionally, honey very occasionally, dried fruit very occasionally, dates and date sugar very occasionally, molasses very occasionally, unrefined cane sugar (sucanat, evaporated cane juice, muscovado, very occasionally, coconut aminos, are okay.
    • algae (chlorella, spirulina), wheat grass (contains wheat germ agglutinin), barley grass, brown rice protein, pea protein, hemp protein, licorice root (except DGL), aloe, slippery elm, chia, flax, lemon balm (tea is probably okay but avoid in supplement form), commercial egg replacers, decaf coffee, herbal sleep aids that contain oat seed, some adaptogenic supplements (ashwagandha is a nightshade), are not okay.
  • Meal FAQ: It is better to eat larger meals spaced farther apart and not snack, unless you have a very damaged gut that can not handle digesting large amounts of food all at once. If you are used to grazing, transition slowly. You should not intermittent fast if you have autoimmune disease. You should not endeavor to be in nutritional ketosis if you have an autoimmune disease (teaser excerpt from The Paleo Approach on this coming soon). You should not eat when under duress. It is better to avoid excessive liquid with your meals, chew your food thoroughly and not rush to the next activity when you eat. You should not eat within 2 hours of bedtime (disrupts sleep). Meals should always include animal foods and plant foods (within the guidelines above), including a quality fat source, and some carbohydrates. There are not firm guidelines for proportion of your meals that are protein, fat and carbohydrate (make sure you get “enough” of each, and then just eat what makes you happy).
  • Useful Supplements:
  • Quality Matters (but it isn’t everything): the better quality food you can source, the better. But if you just can’t afford all grass-fed/pasture-raised meat, wild-caught fish, and organic locally-grown produce, just do the best you can. My post on the importance of grass-fed meat contains some suggestions for incorporating it into your diet in a budget-conscious way. This post ranks different animal proteins to help you prioritize which ones to buy. Whole9Life has a wonderful chart on when fruits and vegetables are in season including which fruits and vegetables are important to buy organic and which aren’t, if budget is an important concern.
  • Your body knows best: If you know that a food that is omitted from The Paleo Approach works very well for you (such as raw grass-fed dairy) or if you know that a food normally recommended on The Paleo Approach does not work well for you (such as coconut oil), then it’s find to modify accordingly. If you aren’t sure or aren’t seeing success, go with the above recommendations. If you find something that truly works for you, whatever it is, stick with it.
  • Reintroductions: Ideally, you should wait until your disease is in full remission before attempting reintroductions (which are discussed in this post). If you are feeling very deprived, you may choose to attempt some reintroductions once you are no longer taking DMARDs or steroids and can see substantial improvement in your disease symptoms. If you do not feel deprived, there is no compelling reason to reintroduce any foods.

Don’t forget the crucial importance of: getting enough sleep (at least 8-10 hours every night), managing stress (mindful meditation is very well studied in the scientific literature and universally shown to be beneficial), protecting circadian rhythms (being outside during the day, being in the dark at night and avoiding bright lights in the evening), nurturing social connection, having fun, making time for hobbies, relaxing, and getting lots of mild to moderately intense activity (while avoiding intense/strenuous activity).

I know from experience that this is a very challenging task. I also know from experience that, in many cases, 90% is not good enough (and the more serious your condition, the more important compliance is until your body has healed). I know from experience that this increases your food budget (although perhaps this can be negated by decreasing your medical expenses). I try to focus on the delicious foods that I do get to eat (yes, there are lots of them!). I try to focus on the fact that I have a strategy for improving my health that is far more powerful than any prescription medication (Note that in many cases you will still need to be on prescription medications, especially those that support organs attacked by your disease, although you may be able to reduce your dose. Please work with your doctor on this one!). And, compliance gets much easier once you start to see improvement (how long this takes will be different for everyone, but typically anywhere from a couple of days to a couple of months). It’s only effort until it’s routine.

Additional Resources

Autoimmune Paleo CookbookWant a great cookbook to help you get started (and while you wait for my cookbook to be released)? The Autoimmune Paleo Cookbook was written by my friend Mickey Trescott.  The print version which was just released contains 150 recipes and the e-book version contains 110 autoimmune protocol-friendly recipes including some wonderful treats (and only 3 or 4 are similar to recipes in the e-book version and about a dozen in the printer version as what will be included in my book, so it’s a great compliment to The Paleo Approach). Read my full review of the e-book version here and see preview recipes here and here.

My friend and functional medicine specialist Anne Angelone has written a set of very handy guides to help you get started, including:

These are great additions to your paleo autoimmune library. And, you can actually get all three and a bunch of other great stuff in Anne’s The Paleo Breakthrough Kit.  This is definitely worth checking out.

newkit2

Consulting Services

Finally, if you find yourself needing help and 1-on-1 support throughout this journey, then I encourage you to check out my new consulting company:

Consulting Logo

Whether you are just beginning your wellness journey or are a seasoned traveler on the wellness path, you may find you need help getting started, troubleshooting roadblocks, optimizing health, figuring out which labs to request from your doctor, or just need support during this major life change. Our consultants can help!

When you work with one of our consultants, you can expect:

  • A thorough review of your health history to establish goals while recognizing obstacles.
  • A fully customized plan tailored to meet your individual needs so that you can reach your goals.
  • Expert guidance to help you navigate your unique challenges.
  • Frequent communication to answer your questions, to adapt recommendations, or optimize your approach as needed, and to provide compassion and encouragement.
  • Concrete strategies to help you succeed.
  • Support every step of the way.

Click here and read the consultant bios to find out how you can get a FREE 10-minute informational consult to help you determine the best choice for you.

Comments

I believe I have a good endo, and I’ve also been taking digestive enzymes for a while. I think it’s a good quality one that contains amylase, lipase, lactase, bromelain, and a few other things. I have microscopic colitis that was diagnosed through a colonoscopy, which is basically inflammation in the colon. It’s thought to be brought on by use of NSAIDs but also has links to autoimmune disease. Because of the colitis I have trouble eating high fiber foods. This makes it difficult to eat a ton of veggies like on the AIp because I’m exacerbating the colitis. Any ideas? Thanks for all support.

I have been juicing and cooking all veggies. It helps, but I’m still having some issues and trying to get to a place of healing.

I am trying to heal too. I am down to trying GAPS introduction diet. Anyone know if you take digestive enzymes with the stocks and broths? Should I only drink the broths for 3-7 days first or is it OK to eat the chicken and fats along with it that I made the stock from? Thanks. Oh leave the vitamins and supplements alone while on the intro diet?

Would you happen to know if anyone has put together a discussion/support forum that is exclusively AIP oriented? Searches are turning up NOTHING for me, but I’d love to be able to easily connect with others for pep talks, recipe ideas and troubleshooting, etc. That’s difficult to do in a basic paleo environment because those not on AIP never remember that we’re off eggs, nuts, seeds, and nightshades :)

Looking for a non-Facebook option, as I’ve already ditched that time-sucking, soul-sucking segment of my life.

Am I out of luck?

I am planning on starting a gut healing diet for my leaky gut issues. Can someone with experience on this subject please tell me how long it would take to heal the gut if one were to follow the recommended diet to a tee? Thanks

Since starting the protocol I have come down with strep and been prescribed antibiotics. What do I do? Antibiotics were part of what got me here but I have to take then for the strep. Do I continue on the protocol? Advice please. Thanks.

Hi, I am wondering if you have more information about why pea protein is not recommended. I have been following a gut healing protocol and am in my 7th week of healing/re-introducing foods. I found a protein shake supplement that I thought would be good because it is complete allergen free/vegan and has high L-glutamine content. The protein sources are ” artichoke protein, pea protein isolate, organic sprouted amaranth and quinoa powders” I realize these are all sources that are not recommended for gut healing/paleo….but will these isolated proteins cause issues? I have been using this for a couple of weeks once a day….and now I’m re-thinking this. I’m thinking it’s not recommended. If you have any thoughts I would appreciate it!

Sarah is not a big fan of pea protein. Peas themselves are a gray area Paleo food and while they may be safe for some people, they are not safe for others. Beef isolate, gelatin, or cricket flour are all “safer” powdered protein sources. – Christina, Sarah’s assistant

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