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!

The Paleo Approach Cookbook is also now available! It provides expert tips on how to make the switch to The Paleo Approach easily and economically. It explains how to stay within your food budget, how to make the best use of your time in the kitchen, and where to shop for what you need. Complete food lists, shopping guides, meal plans, and over 200 recipes take the guesswork out of eating to maximize healing.

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 Autoimmune Paleo Breakthrough Kit.  This is definitely worth checking out.


Also, my assistant Christina Feindel has released an e-book called 28 Days of AIP which contains a 28-day autoimmune protocol meal plan (including several new, exclusive recipes) to help you get started, stay on track, and illustrate that the AIP is a flavorful diet full of variety. Check it out here.

Another great resource for reintroducing foods into your diet safely is Reintroducing Foods on the Paleo Autoimmune Protocol by Eileen Laird. Eileen walks you through the process of reintroducing foods one at a time and gives you pointers on when to start reintroducing foods, keeping a food journal, and how to know if you have a reaction. She also provides recipes appropriate for various stages of reintroducing! Get the e-book here.

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.


Can you please recommend a (non goitrogenic) prenatal brand that is OK for hypothyroidism? I absolutely can’t find ANY information online about this:(

I currently use Garden Of Life but I just realize it has (on addition to goitrogenic veggies), many sprouted grains and seeds. It’s NOT ok for AIP right?

thank you so much for this fantastic info I have been very sick with multiple food intolerances since 1998. was recently diagnosed with celiac and hashi. I react to so many food now, including bone broth, probiotics, some vegetables…but this is the first really comprehensive and smart website that addresses these issues. the docs don’t have this info, even the functional dr I see. (my functional dr. told me to eat almonds, almond butter and take probiotics. when I told her they all made me very sick, she did not know what to do with that info. ) practically all supplements, even the kind doc ordered for me, also made me sick–soy, lecithin, gelatin. Autoimmunity and diet (as explained here) is a delicate balance and unfortunately, it seems, we need to be vigilant about diet. and understand standard healthy protocol (nuts, probiotics) not healthy for all. I do struggle with finding foods I can eat that are healthy for me and fill me up. I am hungry a lot and slightly underweight. I do try for healthy fats. But I am a lot better than I used to be. that’s for sure. been a long road. good to see people like you working so hard to get good info out to public. thank you so much.

Thank you for all the great information. I started a gluten free diet last year after being diagnosed with Hashimoto’s, but only saw minimal results. Last month I began following the autoimmune protocol described here, and can’t believe how much better I feel in just a few weeks. I have been suffering with this disease for at least 15 years, and am extremely grateful to have found information that effectively gives me my life back. THANK YOU SO MUCH!

I am seriously considering starting this protocol (tomorrow, if possible). I’ve experienced all-over body itching for 2+ years now, with a major head-to-toe rash last January, small rash last April and super swollen lips this month (rashes and swollen lips seemingly out of nowhere). And of course, a few doctors and two ER trips have not yet yielded anything helpful, though I did find out I have a mild dairy allergy. Now, for the last 3 mos I have cystic acne and because I’ve been to dermatologist several times over the years for acne (with a course of Accutane in 2005), I have decided to take matters into my own hands. I am not sure I am experiencing any auto-immune issues (no fatigue, joint pain or otherwise, etc) so I do wonder if this protocol would help. Any help/suggestions/feedback would be greatly appreciated!

Janette~ It is possible that you have a histamine intolerance going on. That seems to be the case with me and right now I’m following the AIP diet but also low histamine. Even the freshest meats I can get cause me a reaction so I have to take diamine oxidase supplements too. Even then I can still have problems. There is a FaceBook low histamine, AIP group that may interest you. Also check out the Low Histamine Chef. Good luck!!!

Hi Tina, could you point me to the AIP low histamine group? I am already a member of low histamine chef but didnt know there was an AIP group too.

Phil~ Glad you found it. :-) For those looking fo it, it is a facebook group with the name “Low-Histamine + Autoimmune Paleo (AIP) Help” It is not strictly AIP, but is supportive of all trying to figure out what your body can tolerate food wise.

hi all
you may want to check out Dr Walsh’s research , Walsh Research Institute
I attended a conference two weeks ago – fascinating information and 30 years of research
From what I have understood, High histamines can be connected with undermethylation ( inability of the body to complete the methly cycle effectively(over simplified )and connected to gene expression of MTHFR and other SNP’s
but it gets complicated
Dr Walsh and his group are a front edge organization- science based and while they are focused on mental health- we all know everything is connected
see what you think
And yes, I do believe it goes back to gut and malabsorbtion etc. but sometimes diet isn’t enough
At least that is what i see in my practice
all the best

Hi Katie
Thanks for your comment. I just saw a new functional medicine GP today and he put me onto Dr Walsh as he thinks I have pyrrole disorder. I had the tests today and am awaiting results. I had never heard of pyrrole before, but the symptoms suit me to a T, so I’m keen to see the results! Hope this helps anyone else out there looking for answers.

Sounds like you have leaky gut. I would contact a Functional Medicine MD in your area to help you to heal your gut and get to the bottom of possible food allergies. You’re eating and taking things into your body that are inflammatory and irritating to the gut lining. Hope you find a doctor soon.

Also I am most certain that the Accutane or antibiotics have injured your gut lining. Stay away from any over the counter, etc. meds or drugs. Seriously…your regular western medicine doctor’s don’t understand what their drugs can do the human intestinal lining….NSAIDS, Motrin, Aspirin, Ibuprofen are terrible and can really hurt you and even do permanent damage to the intestinal lining. Get on Sarah’s diet and contact a functional medicine MD!

Thank you for your response! Since the itching started, I have moved to homemade soaps, detergents and remedies and I have stayed away from things like Motrin so I was really hesitant to consider a dermatologist again since I know I would just get put back on harsh medicine. I have spent the day today prepping things such as bone broth, heart sausage and I start the protocol (for sure!) tomorrow. How would I search for a functional medicine MD?

Thank you for all of your help – I did find a functional medicine doctor that I am visiting on Monday. I am already noticing slight improvement, now on my second day of AIP. Looking forward to the rest of the 28 days.

Thank you for offering help Christina…I am not well and couldn’t get back to Janette. I believe there’s a functional medicine association that lists physicians….I think you’d have to google this.

​What’s wrong with Aloe Vera, Flax, Chia, and Hemp?

I’ve read numerous places that Aloe is great for intestinal problems, leaky gut, inflammation. I just started drinking Aloe juice daily, with hopes it will help.

I have Celiac and believe I have inflammation even though I’ve been gluten free for 4 years. I have​ had LGSIL (cervical cell changes) for more than two years, and my body has not ‘healed’ itself of these abnormal cell changes, as is supposed to happen after 2 years. I worry it will turn cancerous. I also have zinc, B12, vitamin D deficiencies, low ferretin levels, hyperproteinemia, and malabsorption. The low zinc and hyperproteinemia is what is leading me to believe that I have an inflamed immune system due to leaky gut– and the fact that I still have cell changes, as well as not the best energy (but my energy is better than it has been for years, nevertheless).

During the past few months I’ve been trying to do research in an attempt to heal my issues. I have been taking really diverse 50 billion strain probiotics daily for the past 3 years, this summer I started on sublingual B12, Norwegian cod liver oil, flax oil pills, vitamin C… a month ago I started taking 500mg of AHCC, and this past week just started on L-Glutamine, vitamin E, and Aloe Vera juice. I am going to start on digestive enzymes soon. So, I am on a lot of the supplements recommended above.

I am not on a paleo diet, per say. I was vegetarian for 10 years (since age 13– I am 24 now), and vegan for 4 (2009-2013). I returned to vegetarianism (almost no dairy, just eggs and butter), more than a year ago, and then 6 months ago started eating fish again, so I am now pescetarian, dairy free (except for eggs and butter– I tried Keifer for its cultures but had a mucosy allergic reaction), and gluten free. I am on a very low budget and am in a very intensive school studying architecture, so I am a little stressed out, but try to manage my stress with moderate exercise (biking, occasional yoga) and meditation (every few days– could be better). It’s very hard for me to afford all of these supplements, and because I am at the studio all day, it’s quite tricky to eat on such a budget (no fridge for lunch/ dinner storage).

My diet has been eggs, gluten free bread, and vegetables for breakfast, rice or quinoa and vegetables– sometimes salmon– for lunch, and vegetables, salad, or soup for dinner. For snacks during the day I eat raw broccoli, carrots, bananas, apples, rice cakes, and almond butter. I have read your blog thoroughly and am aware of that quinoa, rice, almond butter, eggs, gluten free bread– are all not great if I have inflammation or a potential leaky gut. Do you think eating quinoa or GF bread with enzymes would be okay?

After reading more today and talking to a Chinese herbalist, I am going to cut out nightshades (I tend to eat tomatoes often, and potatoes and peppers occasionally), and I will try cutting out eggs (though the thought of it makes me sad). I’ve been trying to lower my coffee intake, but have been drinking it for 6 years, so I get headaches and am moody if I don’t drink it for one day (I am also in school, so I really need it sometimes for classes or studying). I am down to 6-8oz of coffee/ day and then drink green tea. It’s going to be very hard for me to cut out rice, since it is the cheapest and most readily available food near my studio. Can you suggest an alternative? The problem is I have no fridge at my studio so it’s hard to bring anything other than quinoa or potatoes (will be switching to sweet potatoes though)– I find veggies go bad by lunch or dinner time– so I usually just buy rice and avocado.

I apologize for the long comment, but I find your blog very informative and would value any advice or insights you may have. One thing that I don’t think I can do is start eating meat again. I would like to try other alterations first, eating meat would be last resort. I think I should probably eat more fish, though.

Tina, what professional could help me to figure out if I have a histamine intolerance too. I eat organic grass fed meats, organic chicken, pork, goat and rabbit. I have a leaky gut and many food intolerances. I do have a functional medicine md but not sure if she understands the issues totally. I have a fungal overgrowth and poor pancreatic function and take digestive enzymes that come from a fermented source I believe….I have diarrhea pretty much every other day. I am so frustrated. What professional could help me?

Look for a licensed Naturopathic Doctor (the key word being licensed). Licensed NDs go to accredited naturopathic medical schools. Really understanding what is going on in the body, getting to the root of the problem, and understanding the healing processes are at the core of their training – something they are steeped in for 4 or 5 years of school rather than being an certification that is added on later.

Can you tell me who can diagnose a histamine intolerance? I ate some fermented cabbage yesterday and I had diarrhea immediately. I have a fungal overgrowth that’s pretty advanced too. Not sure what’s going on.

Hi Ann~ Sorry for your problems. I can relate. From what I’ve read, diagnosing a histamine intolerance isn’t very straight forward. There isn’t a lab test that is reliable. I have posted some histamine intolerance resources on my blog. You can scroll down to the Histamine Intolerance section and do some reading. That will get you started: There is also a FaceBook group that is low histamine AIP. I posted the name up by Phil’s question a few questions back. Good luck!!

Very interesting about the Histamine issue….my father has histamine allergies but what’s interesting is that I am a poor methylizer and acetylizer…but I don’t have the bad MTHFR gene. I am missing the glutathione gene plus on the Cytochrome P450 system I can’t process certain drugs that use the CYP219 gene snp. Plus I have problems with the 1A1 and 1B1 gene snp’s. Both parents passed on genetic defects. I also have the HLA DQ2 gene…I found this out a few years ago and I am 56 years of age and had been eating wheat and gluten for all that time injuring my gut lining. I am not certain if I have the histamine problem.

Anne how did you find out about your genes? did you use 23andme or some other way to test them? I would greatly appreciate knowing this cause I am wondering how others are doing this .. I am hoping to find if there is any alternative to 23andme people are using .. I didn’t like their privacy policies when I looked into it.. if anyone has other methods to get this kind of genetic testing done I would love to know !

I have severe endometriosis and suspected Sjogren’s syndrome. Is this diet likely to help with Sjogren’s? Does anyone have personal experience with improvement/remission? I would like to know if this autoimmune disease can be halted or reversed. I am desperately seeking answers.

I purchased “The Paleo Approach” as an e-book. The material is excellent. However, it is very difficult to find/access specifically what you’re looking for in the e-format. Also, the charts are difficult to read. Is it possible to get a credit for the e-book to put towards a hard copy book? I’d REALLY to have a hard-copy in hand for the numerous times I have a question and could go directly to the info I need. Thanks.

Jay I would go to a Functional Medicine MD and then they can run tests on you. I had a Detoxigenomic Profile performed on me 5 years ago by Genova Diagnostics. I am very ill today. Hope this helps.

Jay I also had a 23and me genetics test too before all of the red tape…lucky me. You might ask your doctor for an MTHFR blood test too. Many people have this problems and can’t process folate..due to genetic defects. Also get tested for the HLA-DQ2 or 8 gene…for gluten and wheat sensitivities.
I am on the GAPS diet exclusively for a damaged and very leaky gut. I have a fungal infection that has spread from the stomach down into the intestines and it digs into my intestinal lining…not sure if I will ever be able to heal my gut now.

I WOULD LOVE the answer to this because I too have just received my Hashimoto diagnosis and I LOVE IPA and stouts and this will be my saddest challenge! Obviously our health comes first, but honestly, I am reading all of this and it is overwhelming. The good news is I am not crazy! But I am angry. I am angry that I have had hypothyroidism for years but NO ONE ever told me about Hashi. I also need to get tested for celiac disease again as years ago I tested positive for the antibodies, but never had the biopsy. After several years of gluten free diet and still having issues, I had a biopsy (after eating gluten again for a month) and the MD said biopsy clear so eat on! And I have. Now I have an autoimmune disease and it sucks. I am grateful to be on the track of healing, but I am angry that it has taken years! SInce 1996, I have never felt my best. I am sad, frustrated, and sick of conventional MDs. However, I can’t afford a Natural MD. UGH

Can anyone recommend how to get 1300mg of calcium per day on this eating approach? I have rheumatoid arthritis and osteoporosis. Also, does anyone have great breakfast ideas?

I make a green smoothie every morning, celery, dandelion greens, chard or kale with a handful of frozen pineapple and a smaller handful of unsweetened coconut flakes. There is lots of calcium in those greens if you need more make a mid afternoon smoothie. An hour after this smoothie my fav breakfast is chuck roast or sausage with a piece of yam and 1/4 of an avocado.

Hi Sarah,

I heard your interview on the Autoimmune Summit this week. It was great. I recently began following your AIP and it has helped somewhat with my symptoms of Ankylosing Spondylitis. I am interested in using antimicrobial herbs to address any infections that may be contributing to my condition – Klebsiella pneumoniae, shigella, chlamydia trachomatis and other gram-negative bacteria are known to be associated with ankylosing spondylitis. I am reaching out to you because you seem to have the knowledge of, skills with and access to the medical literature, which I, as a lay person, lack.

Do you know anything about this issue, or can you point me in the right direction to educate myself about it? I plan to see a functional medicine doctor as soon as I can, and am saving every penny I can to accomplish this, but unfortunately after rent, bills, student loans, and food, it i going to take some time to get the money together for a consultation, let alone any testing that needs to be done. So I am inclined to try and learn what I can in the meantime.

To be clear, I am not asking for medical advice, simply if you are aware of any good information on this subject.

Thank you so much for any help you can offer.


Sarah advises medical treatment for any infections, which may include prescription drugs, supplements/herbs, or a combination of both. She has not written about using herbs exclusively. – Christina, Sarah’s assistant

My two year old son was diagnosed with leaky gut via IgG and stool analysis. We sought help because of his eczema and digestion issues. We started him on the GAPS diet two and a half months ago. Almost instantly his symptoms got worse. We couldn’t have ferments because they seemed to cause irritation. Probiotics did the same. We never introduced nuts either out of fear.

Day 20 into the diet he broke out in full body hives that lasted for three days. The day his hives went away his eczema looked better than ever but that didnt last long. It has been downhill ever since. His eczema is spreading and it is really itchy (which never used to be the case). Hes up all night tossing and turning and itching himself crazy. His digestion never improved either. For perspective, he has had at most 8 solid stools in his life. Digestive enzymes were helping for a while but they seem to have lost their power.

We are at a loss for what to do now. The gaps diet literally ruined my son. Some people I have talked to thought it could be a mast cell activation syndrome and/or a histamine intolerance. The catch is I took two months off work to try to heal my son but now I’m back at work and hes in daycare. I dont see how the aip protocol can work for a two year old who is in daycare who also reacted so poorly to the gaps diet. If you or anyone has any suggestions I would more than appreciate it. We are desperate for answers. Thank you.

I am so sorry to hear of your son’s troubles. I feel for him (and you). The idea of histamine intolerance and/or mast cell activation syndrome is truly something to consider.

Probiotics didn’t work for me (also caused agitation). When I ate some fermented foods while traveling (before I knew of histamine intolerance) I got very sick. So I can relate. I’ve not tried fermented foods again and I am not taking probiotics.

You could try a low histamine diet, which is mostly straightforward. Here’s one link:

And my blog has more links on histamine intolerance. Just scroll down a bit:

Here’s some info on Mast Cell Activation Disorders (I hope this link works….since I’m logged into it, I’m not sure….)

Good luck,

I have had a 23andme genetics lab test that show many defects in my body…COMT and MTHFR plus many more gene variations. I am completely missing the glutathione gene…no wonder I had so much anxiety and problems with sulfa drugs, epinephrine, and more chemicals, etc. More money needs to me spend on genetics research.

Hi there, I’m Susie and I have Myathesia Gravis, for about 8 yrs now. I have started to elimate grains, sugars and try to eat whole foods no processed foods etc. I take immune suppresent drug Imuran and predisalon along with anti depresent drug Lovan, Mestinon for MG muscle weakness during the day maybe up to 4 a day. I am wanting to know if I try to increase my immune system am I increasing my body’s action to MG ? Muscle weakness in arms, legs and eyes ?thanks

I am curious if you have had a leaky gut test done through Cyrex Labs and also a blood test for either the HLA DQ2 or 8 gene. I would also get a 23andme test done and merge the raw data with Genetic Genie to find out what genetic defects are in your detoxification genes.
Just a start to find out answers to your questions. I never knew I was not to eat gluten or wheat and I had a celiac blood test that was negative, but I wasn’t eating wheat at the time. I never had a biopsy either. I don’t eat wheat anymore and have a damaged gut lining from drinking alcohol. There are certain foods that are very inflammatory to the gut lining..that cause the gut to leak. Western medicine is so far behind Integrative and Holistic its not funny any more.
I wish more money was being spent in Genetics research….had the research happened for me 40 years ago I wouldn’t be as sick and where I am currently at Health wise.

Hello, thanks for all this info, which I too found after ‘the autoimmune summit’. I’m confused about lemon balm as this is written about in many places as a treatment to help with Graves disease, and here it appears as something to avoid.
Many thanks for any clarification,

Are there any protein powders that are allowed? I use to mix unjury protein powder in my fruit and veggie smoothies. It is whey, which I understand is a no no. Any suggestions?

I am making bone broth from locally processed deer- this is the only successful red meat my son can eat-(Crohns). Can I save and use the tallow for cooking? How would I store it?

I couldn’t find this addressed anywhere else, so here goes: I’ve started the AIP with the rest of my family (we all have issues) and my older son has had allergies, eczema, and asthma pretty much his entire life. He’s started losing patches of hair, and his thyroid is showing signs of strain. He’s seven. Here’s what I’m wondering: the allergist told us that he’s got pretty much every environmental allergy there is (pet fur from pretty much all mammals, dust, pollen, mold, grass, pick a tree, he’s allergic). Will his immune response to the environmental allergens he can never avoid (because he still leaves the house for school and stuff) prevent the AIP from really healing him? He’s not super-excited about giving up all his favorite foods, but he’d love to be able to run and play sports and feel good. How do we calm down his immune system with all this other stuff he reacts to? Is the food change enough?

It’s possible addressing diet and lifestyle factors will balance his immune system enough to reduce or eliminate environmental reactions, but everyone is different. – Christina, Sarah’s assistant

Jean~ Have you tried nasal/sinus rinsing for your son (eg Neilmed)? That might help him a lot. I was just talking with a friend of mine who had lots of allergies and he said it changed his life (and he’s a doctor).

Thanks Tina! When he flares, he gets headaches, bald patches on his scalp, and a deep cough (lungs rather than his sinuses) so that probably wouldn’t do much for him. But I do appreciate the suggestion!

I have a question regarding fermented foods. I know kimchi has many health benefits, but it does contain chili peppers. Would someone with autoimmune disease need to avoid it even though it is a probiotic food?

I guess most people don’t understand that alcohol damages the intestinal lining…I know it did for me. People who drink and have metabolic syndrome…that I’ve been told…have leaky gut which is related to autoimmune issues.

5 years of research and I am on 2 to 4 egg’s a day, raw with shells and shell membrane to get the collagen type 1, 4,5,&10 (primarily collagen 1 which makes up 90% of all our collegenetic tissue) I have eliminated most of my joint pain, neuropathy and raynaunds has cleared and is all but noticeable, my feet were flashing red to purple, skin was translucent and you could see the blood vessels, now they are white, eliminating egg’s from diet, Especially raw egg’s (few people are allergic to raw eggs) makes no sense it has the collagen’s in full 3d molecule form which as we age we no longer make but can replicate in the pryors patch, each of these molecules the immune system looks at transports to the lymphatic system and liver and turns off attack to the primary collagen type 1, thus now not only does the AI stop, but you are now making new collagen to heal damaged area’s, — short of being at the Co-Op, when cow’s are killed and standing in a bib with chain saw in one hand and fork in other with bbq sauce on rail – just how do you propose we can get the main LIVING collagen type 1 being attacked in 90% of these AI conditions ? we have 28 collagens in us and each plays a role, but most are directed to support and form collagen type 1, I see no other sterile source other than the whole eggs, in our modern diet that can be stored for long periods of time ? 1:30,000 or %0.00003 chance of reaction or pathogen would take you 86 years of searching for a contaminated to find just 1 under modern FDA regulated packaging requirements, plus the Egg is the #1 primary food which all other foods are nutritiously judged, (IE if milk contained XX grams of protein that amount is judged against how much is in the egg, while so people that have gut problems this might apply to this is a pretty far stretch for 99.9% of the global population starting from 5,000 bc when egyptians first domesticated the modern chicken ! 1 banana, 1 whole egg shell and all, 1 cup ice, and blend for 2 min’s, for a yummy shake and by by AI !!!

PS, I have used ice cream, vanilla, coconut, pineapple and made the mistake of using 2 bananas with vanilla ice cream and caramel and coconut all at once and wife drank all most all of it, (she isnt sick but dosnt miss two a day) tasted like really rich candy, so I don’t make em that tasty any more

Arthritis:( & 100 subsets of it )from young age Injuries-abraded and dead cartilage, tendon, bone, and collagen’s involved (type 1 & 2) possibly others are released into the body, T cells – attack these as they are not where they are supposed to be, (Joint capsule and synovial lining sac) this is stage 1, (300-500 days for full repair) no one takes even a break to give time for proper healing like a broken bone would require !, T cell’s pass along they just Attacked (took out the preverbial garbage cells) these cells and pass along the dna chemical Identifier’s and each following generation of T cells now are alerted to watch for this type collagen cells, IF they continue to find more the Thymus Will become involved after several generations of T cell’s involvement this is stage 2, (you are noticing aches and pains and probably taking otc’s and pressing yourself harder to stay in shape) as you continue the abrasions more and more of the T cells subset MAC complement system becomes involved, this is stage 3, and by now you probably have seen a doctor or 5,. By now with Thymus involvement their is little chance for immune clearance to take place and far more likely of bone marrow picking up the DNA chemical ID’s, thus making pre programmed immune system cells, T, B, Complement etc.., by now you have been in no doubt you are vary sick and need help with nothing but a long list of mis-diagnosed conditions this is Stage 4, and is why you are here now reading this, and while the description above applies to me and million’s of others there are over 1,000 known pathogenetic (environmental, chemical, biological causes and counting) (over 100 named conditions and counting ) But this is of little interest to us, as the concentration is now on just the immune system attacking the collagens of our bodies, Namely type 1, Type 1 makes up 90% of all of you and your collagens and about 90% of immune systemic conditions, so how do you turn it off ? and that is the question? answer is simple you ingest living molecules of collagen’s being attacked, they are Identified in our Peyer’s patch as Food and since our immune system cannot attack something we have eaten the AI is put in check, (not cured-cure would be a bone marrow transplant from stem cell regrowth and you would have to be re-immunized for every condition from childhood up)
It does NOT matter how this type attack turns on, the fact it effects virtually ever organ, from skin, arteries, lungs, heart, liver, kidney’s, all are AI attacks from complement system attack, and can become MCTD at any time for no apparent reason thus we have people that starts out with simple stage 1,2, RA or OA, or OP and wind up with attacks on above listed organs joint’s tendon’s the list is endless of where all type 1 collagen is found
Find the Collagen’s to ingest and you are in remission in 4 hours, heal up in 3 months, good luck to us all

Hello! I recently started the AIP diet (about 8 days ago). I am pretty sure I have candida and sibo. So I have been trying to limit the very starchy veggies. I do not do well low carb, so I have been trying to eat lots of root veggies. As the days have gone on, my stool has gotten smaller and thinner. I would imagine this has been caused by my change in diet. I had a colonoscopy last Feb, and it was fine. I also was having generally regular movements prior to this. I do not digest my food well, so I have been trying to eat mostly cooked foods, and I am also on digestive enzymes. Do you have any suggestions as to help the bowel thoroughly purge? Would adding more carbs help? If so, what carbs based on my condition?

Dont feed the yeast,
All carb’s are broken down into sugar’s, anything with a “tose” on the end turns to sugars in the bloodstream, thus you are limited to protien’s and fresh calorie limited foods like celery, lettuces, raw Broccoli, fruits and veggies like potatoes, tomatoes, = sugars, get on Lactobacilli, and probotics for digestive tract to control this, I had it systemically and was limited to only proteins for 3-4 months before I could add carb’s back in -look up candidia diets, took me months to get back on track

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