Home Auto-immune disease The paleo diet variation to treat auto-immune disease

The paleo diet variation to treat auto-immune disease


The Auto-immune Paleo diet

(Click here for a list of autoimmune diseases)

This post covers:

  •  A brief introduction to the conventional view of auto-immune disease, causes and treatment
  • An brief outline of Cordain’s theory of auto-immune disease and the link to agricultural foods
  • The food you need to eliminate if you have an auto-immune condition. (You may not need to eliminate these foods forever, however I recommend you strictly cut these foods from your diet for 4 – 6 weeks to see what impact it makes.)
  • Links to interviews and videos
  • Links to previous posts on auto-immune diseases and the paleo diet

My next post will cover in simple explanation of Cordain’s theory of auto-immune disease and how the food we eat contributes / or even causes an auto-immune reaction in genetically susceptible people. Plus links to success stories in real people, and tweaks that some people have found successful.

What is an auto-immune disease?

From the American Auto-immune Related Diseases Association: “One of the functions of the immune system is to protect the body by responding to invading microorganisms, such as viruses or bacteria, by producing antibodies or sensitized lymphocytes (types of white blood cells). Under normal conditions, an immune response cannot be triggered against the cells of one’s own body. In certain cases, however, immune cells make a mistake and attack the very cells that they are meant to protect. This can lead to a variety of autoimmune diseases. They encompass a broad category of related diseases in which the person’s immune system attacks his or her own tissue.”

“The immune system normally can distinguish “self” from “non-self.” Some lymphocytes are capable of reacting against self, resulting in an autoimmune reaction. Ordinarily these lymphocytes are suppressed. Autoimmunity occurs naturally in everyone to some degree; and in most people, it does not result in diseases. Autoimmune diseases occur when there is some interruption of the usual control process, allowing lymphocytes to avoid suppression, or when there is an alteration in some body tissue so that it is no longer recognized as “self” and is thus attacked.”

Particular autoimmune disorders are frequently classified into organ-specific disorders and non-organ-specific types. Autoimmune processes can have various results, for example, slow destruction of a specific type of cells or tissue, stimulation of an organ into excessive growth, or interference in its function. Organs and tissues frequently affected include the endocrine gland, such as thyroid, pancreas, and adrenal glands; components of the blood, such as red blood cells; and the connective tissues, skin, muscles, and joints. Some autoimmune diseases fall between the two types. Patients may experience several organ-specific diseases at the same time. There is, however little overlap between the two ends of the spectrum.

In organ-specific disorders, the autoimmune process is directed mostly against one organ. Examples, with the organ affected, include Hashimoto’s thyroiditis (thyroid gland), pernicious anemia (stomach), Addison’s disease (adrenal glands), and type 1 diabetes (pancreas).

In non-organ-specific disorders, autoimmune activity is widely spread throughout the body. Examples include rheumatoid arthritis, systemic lupus erythematosus (SLE or lupus), and dermatomyositis.

The conventional medical view of what causes of autoimmune disease is also described, i.e no-one really knows:

“The exact mechanisms causing these changes are not completely understood; but bacteria, viruses, toxins, and some drugs may play a role in triggering an autoimmune process in someone who already has a genetic (inherited) predisposition to develop such a disorder. It is theorized that the inflammation initiated by these agents, toxic or infectious, somehow provokes in the body a “sensitization” (autoimmune reaction) in the involved tissues.”

And the conventional treatment, which primarily involves treating symptoms, like drugs to suppress the auto-immune response or the inflammation:

“Of first importance in treating any autoimmune disease is the correction of any major deficiencies. An example would be replacing hormones that are not being produced by the gland, such as thyroxin in autoimmune thyroid disease or insulin in type 1 diabetes. In autoimmune blood disorders, treatment may involve replacing components of the blood by transfusion.

Second in importance is the diminishing of the activity of the immune system. This necessitates a delicate balance, controlling the disorder while maintaining the body’s ability to fight disease in general. The drugs most commonly used are corticosteroid drugs. More severe disorders can be treated with other more powerful immunosuppressant drugs, such as methotrexate, cyclophosphamide, and azathioprine. All of these drugs, however, can damage rapidly dividing tissues, such as the bone marrow, and so are used with caution. Intravenous immunoglobulin therapy is used in the treatment of various autoimmune diseases to reduce circulating immune complexes. Some mild forms of rheumatic autoimmune diseases are treated by relieving the symptoms with nonsteroidal anti-inflammatory medications. Drugs that act more specifically on the immune system, for example, by blocking a particular hypersensitivity reaction, are being researched.”

Before I was introduced to Cordain’s work, it never occured to me that my own auto-immune problems could be altered in any way except by conventional means. (Note – there very little awareness of diet except with celiac disease in the conventional website) My main issue was joint swelling and discomfort, which reduced with large amounts of omega 3 (anti-inflammatory), anti-inflammatory over the counter drugs like ibuprofen and rest.

The first paper I read that convinced me to cut out grains and legumes is this one by Cordain: Cereal Grains; Humanity’s Double-Edged Sword

Autoimmune Diseases and Cereal Grain Consumption
Autoimmune diseases occur when the body loses the ability to discriminate
self proteins from non-self proteins. This loss of tolerance ultimately results in
destruction of self tissues by the immune system. Autoimmune diseases occur
in a variety of tissues and include such well-known maladies as rheumatoid
arthritis, multiple sclerosis, and insulin-dependent diabetes mellitus (IDDM).
Typically, autoimmune diseases are characterized by the presence of auto-antibodies
against specific self proteins [229]. Most autoimmune diseases are
thought to develop via an interaction of an environmental factor or factors
in conjunction with a specific hereditary component.
Dietary cereal grains are the known environmental causative agent for at
least two autoimmune diseases: celiac disease [230] and dermatitis herpetiformis [231].Withdrawal of gluten-containing cereals from the diet ameliorates
all symptoms of both diseases. Further, evidence from clinical, epidemiological
and animal studies implicate cereal grains in the etiology of other autoimmune
diseases. The mechanism or mechanisms by which cereal grains may induce
autoimmunity in genetically susceptible individuals is not clearly defined;
however it is increasingly being recognized that the process of molecular
mimicry, by which a specific foreign antigen may cross react with self antigens,
may be involved in a variety of autoimmune diseases [232, 233]. Additionally,
cereal grain lectins and proteins may also have involvement in the development
of autoimmunity via their modulation of immune system components.  (Read the rest in the article from page 48)

An excellent interview with Cordain is found here, where he describes the mechanism by which agricultural foods may trigger auto-immune reactions in genetically susceptible people: Loren Cordain – Autoimmune Disease and Food Triggers, Link to MP3 interview with Loren Cordain (45 minutes)

Watch this video of Cordain’s lecture “The Paleo Diet Multiple Sclerosis”


What foods should you eliminate for the auto-immune version of the paleo diet?

  • Gluten grains MUST be strictly avoided. Wheat, oats, barley, rye, triticale
  • All other grains (rice etc) and pseudo- grains like buck-wheat
  • All legumes; lentils, kidney beans, chickpeas, peas, soy and soy products, peanuts …
  • All dairy; cream, butter, ghee, milk, yoghurt, even raw.
  • All alcohol, it is a gut irritant
  • Eggs
  • Nightshades; includes potatoes, eggplant, capsicum, all peppers and chilli, tomatoes
  • Although Cordain does not include these – I’ve noticed many people with auto-immune disease do not tolerate any nuts or seeds, or need to limit them. For this reason I recommend a 30 day trial eliminating all nuts and seeds
  • No sugar or sugar alternatives
  • No chemical additives, preservatives, colours, flavours
  • No vegetable oils

So what can I eat?

  • All unprocessed meat and poultry; no additives, wild or free range, ideally organic.
  • Seafood / fish high in omega 3 oil
  • Include organ meats and bone broths
  • All vegetables, including peeled root vegetables, organic if available (but not nightshades)
  • Sea vegetables, seaweed
  • Fruit in moderation, especially berries. Fruit is best eaten at the end of a meal so it doesn’t elevate blood sugar too much
  • Include fermented foods, like sauerkraut to improve gut bacteria
  • Healthy low omega 6 oils; cold pressed from olives, avocado, coconut and palm
  • Meat fats; lard, tallow, duck fat
  • Avocados and olives
  • Coconut cream without guar gum or other additives (these are legume derivatives)

More from previous posts on Auto-immune conditions and paleo eating;

Dr. Jean Seignalet, ancestral diet and auto-immune disease trials
Auto-immune disease HLA-B27, client pain free on no starch, paleo diet
Remission of auto-immune disease, Lupus with Paleo diet
Hashimotos, Auto-immune thyroid disease, avoid gluten like the plague
My Mum’s lupus / small airways disease improve on paleo diet!
My 30 day strict alcohol free auto-immune paleo diet


  1. Very good post.

    I’m having good success eating rice, skinless potatoes, scallops, and a rotation of other lean meats.

    I don’t have your exact symptoms, but get autoimmune reactions from most of the things you posted.

      • I recomend that rice be avoided for the first 30 days on paleo – then IF you need extra starch AND you do not react in any way to it – rice is usually not a problem. White rice has very low anti-nutrients and cooking reduces them. See perfecthealthdiet.com for more on rice as a safe starch.
        Personally I eat rice very occasionally.

  2. By the way, vegetable matter gives me a hard time, probably due to gut bacteria issues. So I avoid anything with plant fiber.

    I’d recommend Kombucha instead of sauerkraut for that reason. I’m growing some now, we’ll see how it goes. The key I think will be to let the kombucha set until all the sugar is gone.

  3. Really interesting post Julianne,

    I was surprised to see eggs on the list – they’re something I’ve been eating more of since giving up the dairy. Would be interested to see if I feel different by cutting them out.

      • Julianne:

        I’ve been continually surprised at how little most doctors understand about autoimmune diseases, especially rheumatologists. The treatment programs I’ve seen are universally as follows: “Start with prednisone, increase the dose until you can’t sleep or function in daily life, switch to more and more toxic medicines as symptoms worsen, and hope the drugs don’t kill you before the disease. No, you can’t change the course of the disease by anything you eat, drink, or do.”

        Moving on: I take that Cordain article about eggs with a grain of salt. It claims that “Egg white allergy in the general population varies between 1.6 – 3.2 %”, which is absolutely untrue.

        Actual figures for egg allergy among young adults 20-45: “The prevalence of probable IgE food allergy was: <0.27% for wheat, 0.09% (95% confidence interval = 0.0 to 0.49%) each for cow's milk and egg, 0.53% (0.21 to 1.09%) for shrimp, and 0.61% (0.25 to 1.26%) for peanut." (source).

        0.09% is a long way from 1.6% – 3.2%.

        As far as Cordain’s contention regarding lysozyme transporting other proteins through the gut in significant amounts, he himself admits in a comment that this isn’t actually a proven connection, and that more research is necessary (which the article promised would appear in 2010).

        There’s an important difference between “plausible” and “proven”. This doesn’t mean no one should experiment with eliminating eggs – but I think the evidence shows that it’s a low-percentage play.


        • Thanks JS, I’ll look at the egg issue a bit closer.
          One group that seems to get more impact from eliminating eggs are those with psoriasis.
          I too think eggs are less of a problem than other foods.

          • Hi Julianne,

            So are you saying that eating eggs might contribute to psoriasis? I tested at a level 2 for eggs (4 being the worst/highest) on an iGg delayed food allergy test and I do have a few patches of either psoriasis or eczema that I cannot get rid of.

          • Yes – eggs are a problem for some – try removeing them for a few weeks and then a trial adding back in. Nightshade foods are a big issue for some with auto-immune disease too

  4. Hi, Julianna,
    Thank you for linking to my interview with Loren Cordain and for summarizing the key points. Yes, it’s a long list of foods that Loren provides cautions about when someone’s gut may be compromised, but fortunately there are plenty of other tasty ones left!
    Another issue that’s worrisome, but fascinating at the same time, is the persistence of these issues. An expert from the Celiac Disease Center at the University of Chicago mentioned to me that IF someone has an autoimmune reaction to glutens, eating some of that kind of food can lead the immune system to keep attacking the gut for several weeks. That is, the problem is not over once the food leaves the digestive system, or even in 10 days, the way that catching a flu bug tends to make someone sick for a couple of weeks and then settles down. He says the immune system confusion – and attack against body organs – can persist for weeks and weeks. It’s a disconcerting rationale but also one that’s motivating for why some people truly are better off never having “just a little taste” of foods that mess up their immune system response. I wish we had better ways of determining just what those foods are for each of us! I’d be curious what you think of that. The interview is at:


  5. Perfect timing! I had just pulled up that Cordain lecture for a friend who’s family is dealing with MS. I’ve suggested this diet (I don’t think I mentioned buckwheat and rice… hmmm) to another friend of the family who’s son has juvenile RA. I know he has found it restrictive, but was doing well over the summer, before returning to school and the land of gluten-filled treats.

    • Yes – it is tough with kids, one of mine 15year old is very controlled now, and the other not. In New Zealand we do not have school lunches fortunately – so all kids take their own. At least that gives more control. Let me know how if your friends have success on paleo if they use it with their atuo-immune issues.

    • Hi, Victoria,

      If you have a friend with MS, you might also be interested in Ron Rosedale’s take on autoimmune diseases such as MS. Ron emphasizes the importance of eating in a way that reduces the chance of cellular resistance to hormone signalling – with Leptin and Insulin to hormones that are important to keep low. I’d be interested to see what you all think of his ideas — they’re in this interview about neurodegenerative diseases and diet:


  6. Very satisfying for me to read the scientific explanations behind statements such as wheat contains opioids and how bacteria/viruses can help trigger autoimmune diseases. Cordain’s writing has certainly given me food for thought! Thanks very much for publicising this.

  7. Out of interest, I had HLA-DQ testing done by the American Red Cross (via enterolab.com) and the result said I had inherited at least one of the 2 copies of my gluten sensitive genes from each parent. Mum had Scottish/Irish blood and Dad had Scottish/Welsh blood. These genes were analysed to be the HLA-DQB1, Allele 1 0202 and Allele 2 0501 with the serologic equivalent being HLA-DQ 2,1 (Subtype 2,5). I got zero response when I told the other 5 siblings which surprised me. I’m wondering if the huge amount of immunisations I had for nursing, overseas travel and a heap of them plus a bout of influenza A in 2005 triggered the Hashimotos.

    • Interesting, I do not know my HLA types, but wouldn’t be at all surprised if it was something similar. My ancestry is primarily Scottish. My mother has Lupus, and I have (or had) similar joint issues to hers. No one else that I know of in my family has Hashimotos though, so like you I wonder what triggered it.
      Interestingly with regards to tissue typing, the 4 kids in our family are so different – we look unrelated. No one else got my mothers Lupus symptoms, just me.

    • I realize that you posted this more than a year ago but I hope it gets to you. I was diagnosed with Systemic Lupus in 1990 by one of the top Rheumatologists in the country. He put me on Plaquenil for a few years and some of the symptoms got better but my life was still significantly affected. I was lucky that a friend brought to my attention a letter in Dear Abby (of all places) from someone who had been diagnosed with Lupus who, it turned out, had a legume allergy instead. I had nothing to lose I thought (though my doctor advised that I could die if I stopped taking Plaquenil) so I stopped eating legumes. Now I didn’t eat dairy at that time or red meat but I did eat tons of soy and lot of brown rice. I stopped all legumes, including of the course the soy, and in a matter of a few weeks ALL my symptoms left. It seems that a legume allergy can masquerade as Lupus! My doctor called it “spontaneous remission”. Needless to say, I dropped my famous doctor and haven’t had any Lupus symptoms since. My present doctors say that it must have been a poor diagnosis but when they hear who diagnosed and how he went about it (blood tests, biopsy, etc.) they just shake their heads. I now pay this information forward whenever I can. I don’t know how often this is misdiagnosed but it’s worth a try. I’ve now been full paleo for a year and have the best health ever in my life. I’m going to try going without eggs and nuts for awhile and see if that doesn’t clear up a skin problem that I still haven’t completely licked but so far, the paleo way of eating has given me such a long list of health improvements that I wouldn’t know where to start. If you have Lupus, I would highly recommend that you at least try this diet for a few months to see if you don’t get relief from your symptoms. I hope you do.

  8. Hi Julianne,

    I have tried variations of strictness for the AI-Paleo (dx RRMS May 2009) protocol and anecdotally don’t notice much of a difference from “Primal” style eating (that I started in late summer/fall 2009) in which I include eggs and full fat dairy (with the exception of tomatoes which I generally avoid like the plague because of GERD when I do eat them). I just recently (~ 1 month ago) reintroduced dairy after about 4 months of total elimination and so far so good. I wonder whether this immunity (pardon the pun) to dairy is because of my genetic background or because I am a bit of a mercenary when it comes to gluten, soy, and processed food avoidance. Likely its a combination of these factors.


    • Yes I don’t think all these foods are a problem for everyone with AI.
      I’ve added some things back in, like eggs which I don’t think are a problem for me. Alcohol is sadly – affects my Raynauds, and dairy makes me break out.

      Strictly eliminating then adding in one trial food at a time like you did is one way to gauge if the food is a problem.

  9. Hi,

    I am from India and am suffering for HS which now people think is an auto immune condition. I just wanted to know what can be had instead of bread or rice as our meals are very different from yours.

  10. I was wondering if the “no sugar or sugar substitutes” included stevia?? Stevia is what my natural doctor told me to use instead of sugars while treating my candida issue. Thanks for your help. 🙂

    • Yes – stevia is derived from a leaf – which makes it natural in one respect. However sweeteners without sugar trick the body – we have sweet receptors on our tongue, when we taste sweet we get ready to digest sugar, and send out insulin in anticipation. It also keeps us in a craving state for sweet. So one should get used to no sugars and no sweeteners. And get familiar with the taste of real fresh food, and the natural sweeteness of fruit for example.

        • I have cocoa unsweetened with a little coconut cream, I weaned myself off sugar with it, and now prefer it that way. I guess if that is all you use it for – it’s not too bad.:)

      • I have to agree 100% with this. The first time I used Stevia I nearly fainted. I got light headed instantly and blacked out and wobbled briefly. I almost fell but caught myself and went to lie down. I told my egg head friend about it and he immediately said it was because my body was expecting glucose and that’s not what it was.

  11. I have assorted autoimmune diseases and am adopting the modified Paleo diet to try and get back into remission. I cannot get omegas from fish/fish products as I am allergic. Are Chia Seeds okay as a supplement to get them???

    • Generally an allergy is to the protein component of a food, not the fat. A high quality ultra refined fish oil shouldn’t have any protein in it – so it is normally tolerated. However you would have to test that to see if you dont react.
      Otherwise use a combination of vegetarian DHA / EPA derived from algae – so no fish products, and flax / linseed oil. That should give you a range of omega 3s. Chia seeds unless you eat a lot ground up are unlikely to give you much omega 3. An auto-immune paleo diet is recommended for a 1 – 2 month trial and this cuts all seeds and nuts as well as grains.

  12. Hi Julienne and others –
    Thank you for publishing all this highly educational information. I have autoimmune issues – eye inflammation as well as joints pain plus gut issues – I am currently in the middle of getting diagnoses/some answers from my doctors. I am looking forward to starting a strict paleo diet to hopefully improve/curb my symptoms.
    I do have a question that no one seems to have brought up before – on such a lean diet, what vitamin supplements should we take? For celiac disease there is CeliAct that, apparently, does wonders for that group of autoimmuners. Would CeliAct be a good addition for someone on a paleo diet since we are eliminating all+ gluten?
    What kind of Probiotic should we be taking – would Culturelle (sp?) Gluten Free work? What about Omega 3 supplements; any other vitamins?? Please help answering this for me, no doctor is helping me out here…
    Thank you a billion times to everyone who has any suggestions.
    Feel better, everyone!

  13. Hi Julianne, really good post you have there 🙂 Was a little confused on the paleo autoimmune protocol but I have a greater understanding on it after reading your post.
    I was diagnosed with SLE and Hidradenitis Suppurativa which is also suspected to be an autoimmune diseases. I’m Asian, and Asians eat lots of rice. It’s kinda part of our staple diet… So to eliminate rice completely is actually really hard for me. Is there any other alternatives to grains?
    Besides that, I have a question. If we actually reintroduce each suspected food group(I suspect that I react to diary, eggs and nightshades the most), is it possible to get a bad flare-up from it?
    I’m currently still healing from my recent horrible flare-up from SLE and also having boils which are not healing cos of the steroids I’m eating… So I’m not starting this diet anytime soon. But I’m interested and would like to start this diet in the future because I have enough of these autoimmune diseases.

  14. Hello

    I have an autoimmune disease And made a test for leaky gut
    (Zonulin) which was negative.
    So my question…
    Can i also benefit from the paleo diet or would be, in my Case, ridicioulus…?

      • Hi
        I made a stool test for Zonuline, Calprotecin and Alpha1-Antitrypsin.(I´m from Germany so the terms could maybe differ)
        I suffer from autoimmune myocarditis for 3 years and no therapy can stop stop the problem so AIP would be my last hope.
        I´m also underweight ( BMI 15) so it will be a hard work.
        What´s about fruits??
        I know, too much would be a problem…but in my case??
        Would it be also detrimental??
        Thank you…
        Many greetings from Germany

  15. Oh I forgot…
    I was vegetarian and now I have to eat meat (lamb) and fish.
    Now I have problems with the digestion.
    Is there any other protein source??

  16. Thanks Juliane ,
    I read that you live in india and I wish to know if there is someone who can help
    With vegetarian paleo or aip
    I have never had meat or bone broth my autoimmune has progressed over years
    From thyroid , rheumatoid , rhitiis etc
    Currently I am suffering form subacute hypersensitive pneumonitis and my lungs are being attacked by an allergen.
    I wish to go off the high dose of steroids

  17. I\’ve done regular Paleo for about 10 years. I had some very good initial results and generally felt better. However, I have struggled to get sustained results with psoriasis. I\’ve been strict and modified to get better results, eventually doing autoimmune protocal for a year (I did still include some nuts and seeds that weren\’t issues in several tests I completed). The truth is I\’ve played with diet and supplements a great deal and cannot find a correlation to psoriaisis. However, I know there is something that triggers it and makes it angry and, in spite of all diet efforts, psorisis is actually worse. What does one look for next?

  18. Hi,

    thanks for a very interesting site. I was diagnosed with Dermatomyositis 15 years ago and after two years of normal treatment went into remission. Just recently I’ve had a bad flare-up and was put on to prednisone. As i want to come off it asap, I have done a lot of research on the Net and to my delight read about so many people who have had great result with correct diet (AIP) which I have now started, and already within a week seen great results.

    One question I would like to ask as no one seems to address this, are “Gluten-Free” products such as Oats etc, permitted? What I am not sure of, is it the Gluten or the actual grain that is the problem? Thanks!

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