The Gluten-Thyroid Connection | Chris Kresser

The Gluten-Thyroid Connection


Last updated on

This article is part of a special report on Thyroid Disorders. To see the other articles in this series, click here.

In the first article in this series, I showed that hypothyroidism is an autoimmune disease in 90% of cases. In this article we’re going to discuss the connection between autoimmune thyroid disease (AITD) and gluten intolerance.

Several studies show a strong link between AITD (both Hashimoto’s and Graves’) and gluten intolerance. [1, 2, 3, 4, 5] The link is so well-established that researchers suggest all people with AITD be screened for gluten intolerance, and vice versa.

What explains the connection? It’s a case of mistaken identity.

The molecular structure of gliadin, the protein portion of gluten, closely resembles that of the thyroid gland. When gliadin breaches the protective barrier of the gut, and enters the bloodstream, the immune system tags it for destruction.

These antibodies to gliadin also cause the body to attack thyroid tissue. This means if you have AITD and you eat foods containing gluten, your immune system will attack your thyroid.

Even worse, the immune response to gluten can last up to 6 months each time you eat it. This explains why it is critical to eliminate gluten completely from your diet if you have AITD. There’s no “80/20” rule when it comes to gluten. Being “mostly” gluten-free isn’t going to cut it. If you’re gluten intolerant, you have to be 100% gluten-free to prevent immune destruction of your thyroid.

So how do you find out if you’re gluten intolerant? Unfortunately, standard lab tests aren’t very accurate. They test for antibodies to gluten in the bloodstream. But antibodies in the blood will only be found in cases where the gut has become so permeable that gluten can pass through. This is a relatively advanced stage of disease. Blood tests will miss the many milder cases of gluten intolerance that haven’t yet progressed to that stage.

Stool analysis is far more sensitive, because it detects antibodies produced in the digestive tract that aren’t yet escaping into the bloodstream. Using this method at Entero Lab, Dr. Kenneth Fine, a pioneer in the field, has found that up to 35% of Americans are gluten intolerant.

In addition to the stool analysis, Dr. Fine’s lab uses a cheek swab to test for the genes connected with gluten intolerance and celiac disease. People with HLA DQ genes are more likely than the general population to have autoimmune disease, celiac disease and gluten intolerance. Dr. Fine’s research shows that more than 80% of Americans have one of these gene types.

When I first read Dr. Fine’s research, I was astounded by the implications. It suggests that 1 in 3 Americans are gluten intolerant, and that 8 in 10 are genetically predisposed to gluten intolerance. This is nothing short of a public health catastrophe in a nation where the #1 source of calories is refined flour. But while most are at least aware of the dangers of sugar, trans-fat and other unhealthy foods, fewer than 1 in 8 people with celiac disease are aware of their condition. I would guess that an even lower proportion of people are aware they are gluten intolerant.

One reason gluten intolerance goes undetected in so many cases is that both doctors and patients mistakenly believe it only causes digestive problems. But gluten intolerance can also present with inflammation in the joints, skin, respiratory tract and brain – without any obvious gut symptoms.

As much improved as Dr. Fine’s methods are, they aren’t perfect. In some patients with autoimmune disease, their immune system is so worn out they can no longer produce many antibodies.

Hashmioto’s, the most common autoimmune thyroid condition, is primarily a Th1 dominant condition. I’ll explain what this means in further detail in a future article. For now, what you need to understand is that in Th1-dominant conditions, the Th2 system is suppressed. The Th2 system is the part of the immune system responsible for producing antibodies. When the Th2 system is severely depressed, the body’s ability to produce antibodies is impaired. The levels may be so low that they won’t show up on a test. So, even if you have gluten intolerance, your test for gluten antibodies may be falsely negative if you have Th1-dominant Hashimoto’s.

This is why I recommend that you avoid gluten if you have AITD, regardless of whether tests show an active antibody response. This is especially true if you have one of the genes (HLA DQ1,2, or 3) that predisposes you to developing gluten intolerance. In my opinion continuing to eat gluten when you have a confirmed autoimmune condition simply isn’t worth risking the immune destruction it could cause.

In fact, the more I learn about gluten and its effects on the body, the more I think we’d all probably be better off not eating it. Mark Sisson has written extensively about the dangers of gluten and gluten-containing grains, so head over there and have a look if this is new to you.

The short version: foods that contain gluten (both whole grains and flours) contain substances that inhibit nutrient absorption, damage our intestinal lining, and – as I’ve described in this article – activate a potentially destructive autoimmune response. What’s more, there are no nutrients in gluten-containing foods that you can’t get more easily and efficiently from foods that don’t contain gluten.

The good news is that if you have AITD and are gluten intolerant, removing gluten completely from your diet will dramatically improve your health. It’s not easy, but it’s worth it.


Join the conversation

  1. Hi Chris, Thank you for replying to all of our comments. My mother has Graves disease and has often suspected an intolerance to gluten, suffering from severe migraines and dark circles under the eyes which I have heard can be an allergy of some sort. I am being watched by my doctor for Graves disease as my thyroid functions higher than normal . I do also have the dark circles under the eyes, depression, joint pains, very lethargic and irritable. I have also suspected an allergy to gluten which I will try eliminating to see. Do you know if a gluten allergy affects kids behavior? My 2 sons have continuously itchy skin(especially their bums), are constantly moody, explosive in temper but, also there is something they seem to eat that make them act with no eye contact, inability to focus, and extremely hyperactive behavior from there normal childlike selves. I am aware of a food dye allergy they have which we have cut out but, are you aware of symptoms with gluten like this? Thinking that it might be an allergy or intolerance in the family.

    • Tiffany, that sends up some red flags to me – lack of eye contact in particular.

      There is a long but totally unscientific comment thread over at the Primal Parent ( with examples of children’s behaviour after eating dairy and grains, which may be of interest to you.

      As daunting as it seems at first, you might want to read up on the backgrounding for the GAPS diet ( and consider taking part in the 30-day intro diet challenge (no, not a weight loss thing AT ALL!) in October over at Health, Home & Happiness (

      Call me a cynic, but I have found mother’s intuition, when coupled with focussed self-education, to be far more thorough in promoting a child’s health than a test run by a doctor. By all means, if your research turns up specific questions, refer to professional help to confirm or rule out your suspicions! In the mean time, as Chris has said above, cut out grains and see if that changes anything. Good luck.

    • Tiffany, I am gluten intolerant and hypothyroid. I am also iron deficient. Since starting on iron supplements my itchy skin (I get ani pruritis, like your sons) has dramatically improved, as has my mood, dry/cracked skin on feet and heavy periods. I just mentioned this because I think the iron deficiency is somehow related to the gluten intolerance, but maybe an iron supplement would help your sons. (Just be warned, it can also cause constipation – I found magnesium effective in dealing with this).

  2. I just wanted to say thanks – your blog (and twitter feed) is my main source of health news. I can also pretty confidently say after having been totally off gluten for 5 months that it has helped with my thyroid symptoms. I’m a Hashimoto’s currently in the ‘wait and see’ place with a TSH of 7-8, tried Levothyroxine and Euthyrox before but it made me worse. I’ve been off medication for about a year and have been having increasing problems with muscle tremors and spasms – but since I cut off gluten they’ve gone away. So I’m definitely not going back 🙂

  3. I had My Thyroid removed last year because they found two hot nodules. I’ve always had a hyper thyroid but not enough for a doctor to put me on meds. This past year has been better as far as my mental state but my body has been doing some strange things. I have developed loss of pigment in my skin and my stomach hates me. I have a doctors appointment this week to see if I’m gluten intolerance and for the pigment loss. My question is, Is it possible for untreated gluten intolerance to cause cancer in the thyroid?

  4. Thanks for the effort creating this blog. I saw almost girl have thyroid, is it through that only girl has the biggest possibility to attack by thyroid? Maintaining gluten – free foods would not be perfectly safe. There are lots of diseases from now on, like Celiac Disease, Hashimoto and this hypothyroidism.

  5. Thanks for the effort creating this blog. I saw almost girl have thyroid, is it through that only girl has the biggest possibility to attack by thyroid? Maintaining gluten – free foods would not be perfectly safe. There are lots of diseases from now on, like Celiac Disease, Hashimoto and this hypothyroidism.

  6. I must add that two of the studies you referenced indicated a 3-5% rate of celiac in those with autoimmune thyroid diseases – hardly compelling.

  7. I read the information in the studies you referenced. Of those, only one indicated an unusually high prevelance of celiac in Graves and Hashimoto sufferers. The last referenced the high level of thyroid disease in celiac sufferers, not the high rate of celiac in thyroid disease sufferers. The overwhelming consensus seems to be that those who have celiac should be monitored for autoimmune thyroid conditions – not vice versa. Granted, getting tested is easy, and might as well – but the leaping to the conclusion that there is a strong correlation based on these studies is a bit much and makes me skeptical.

  8. thanks for the great info! I was  diagnosed  6 weeks ago w/ gluten, dairy and corn intolerance/allergies, low Vit D, hypothyroid, overactive adrenals, and low protein levels. I’ve been gluten and dairy free since the diagnosis, and mostly corn free except where corn by-products occasionally slip in (e.g. dextrose.), and am on thyroid supplements. I feel better than i have in years!  lots more energy, skin rashes are clearing up, depression is lifting.    I loved reading your posts about the interrelationship of these conditions– i was wondering if there was a link.
    And i’m curious about the grain connection.  I’m a botanist, and know that most of the common grains (all?) (rice, millet, wheat, ancient wheats, corn, teff, etc.) are all fruit (seeds) of  plants that are botanically grasses, and are more broadly classified as monocots –a group of plants that includes lilies, orchids and grasses.  Buckwheat is in a completely different classification–it’s a dicot, or broad-leaved plant.  Is it something about monocots that makes them harder to digest or more likely to cause an immune response?  i’m thinking about other plants that we eat, and almost everything I can think of is a dicot. (coconut being another exception–it’s a monocot–as is ginger, lemongrass, and turmeric.) Just curious as to whether you have any thoughts on this, or know of any research about it.
    Anyway, i’ll definitely be sharing links to your site with friends and family members.  thanks for the great articles and detective work with putting all this together.

    • I think buckwheat is well-tolerated in most people. I eat it myself, usually in the form of buckwheat crepes (recipe). I’m not aware of any specific research suggesting dicots are better absorbed than monocots. Please let me know if you find any!

  9. Great Article!  I was diagnosed with hypothyroid 18 months ago.  I have lots of joint pain/muscle aches.  That has been my biggest symptom (I have obvious ones too) & docs keep looking at me like I have 10 eyes.  The symptoms come & go & I can’t seem to regulate my thyroid (even when I stay on the same dose for a long time).  I’m wondering if something else is making my thyroid fluctuate (ie. gluten) & I know that the joint pain / muscle aches are common in gluten sensitivity.  I was tested for celiac & it came back negative.  I took an immuno blood lab test & wheat was a +1.  So, I’m wondering if I really do have it & whether it’s worth going off gluten for 6 months.  Any thoughts?

    • I suggest all people with hypothyroidism (and probably just all people in general) should be off gluten forever.

  10. Excellent article and follow up conversation.
    Selenium can be measured functionally using a lymphocyte proliferation assay (spectracell labs does a good job with this).  Additionally reverse T3 can be measured as a marker for selenium deficiency as it is required to convert T4.
    Looking forward to the next article.
    All the best,

  11. Thanks for your comments Chris and I’m glad to hear your suggestion about eating buckwheat. For anyone beginning a gluten-free diet, buckwheat is actually an herb (Fagopyrum esculentum ), not a grain at all. And it has some amazing nutritional properties compared to the basic line-up of gluten-free flours (rice, sorghum, millet, tapioca, cornstarch, potato starch.)
    Two substances in buckwheat are being studied (I think at Cornell?) for their positive effects on blood glucose regulation – “D-Chiro-Inosito” and “fagopyritols.”
    But I’m wondering why you don’t believe dietary goitrogens have a significant effect on thyroid dysfunction? In populations with iodine def with diets high in grains like millet, goiters and thyroid disease are epidemic. Do you mean dietary goitrogens don’t significantly affect thyroid function in populations with adequate iodine status?
    I’ll look forward to reading your article (which I hope will discuss halogens and thyroid dysfunction.) Thanks again Chris.

  12. Wow. What a great discussion. I’m thrilled to have found your site Chris! I’m a gluten-free cooking writer and have had a recent email conversation with a reader about several gluten-free grains and starches (tapioca, aka. cassava root, millet, teff, sorghum and soy) which may have goitrogenic effect on the thyroid gland. I am just embarking on a search to learn more about this potential effect.
    PubMed search results for “cyanogenic glucosides in cassava, millet, sorghum” and “goitrogens in cassava, millet and sorghum” turn up little (very little, like a mouse study and old studies done in the Sahara and Nigeria, where populations consume large amounts of millet and cassava.)
    Chris, do you have insight into the potential thyroid-suppressive effects of any of the above mentioned gluten-free flours? As someone with non-celiac gluten sensivity (diagnosed through Dr. Fine’s Enterolab,) Hashimoto’s hypothyroidism and casein intolerance, I am increasingly convinced to adopt a Paleo diet, avoiding gluten-free grains in the process of seeking real health.
    Thanks again for your enlightening work.

    • Teri,

      I don’t believe dietary goitrogens are significant contributors to thyroid dysfunction – although environmental goitrogens are. I will probably write about this in a future article.

      That said, as you well know there are many who believe grains aren’t a good idea because the anti-nutrients they contain. The only grain I eat these days is in the form of very occasional sourdough buckwheat crepes – and buckwheat isn’t technically a grain.

      • Just thought I’d add a Gluten free sprouted buckwheat and Quinoa bread (no yeast) Recipe
        >Quinoa is high in protein>
        >Sprouting the grains starts the breaking down of protective proteins making it easier to digest.
        >Sprouting and the Bi- carb of soda makes it Alkaline…which is better if there is Inflammation in the body!
        2 cups quinoa
        2 cups of buckwheat
        Put grains into bowl, wash and then put just enough water to cover and stand overnight.
        In the morning process in a food processor or I use an Oscar juicer (mincing option)
        Add a little water needed to make it thick enough that it can pile up in a hill without flopping.
        Add about 3 teaspoons of bicarb of soda ( or any raising agent you wish)
        And bake straight away in a baking paper lined bread pan, in a 180- 200 degrees oven, for 1hr and 1/2.
        Turn out of pan after 10 mins and place without paper on a wire rack, let cool.

        • Opps forgot to mention you can add Salt, nuts and seeds…
          And In the morning the seeds will have sprouted little tails..dont sprout for much longer or it wont work!

  13. Chris- I’ve recently discovered, by accident, that gluten is creating havoc in me.  In Nat’s comments of 7/19, she states that she “knows when she’s made a mistake cuz the next day she has stomach cramps and the spots come back all over her body.”  I have these brown spots which began a few years ago, and the majority of them are under my arms and inner thigh areas.  I’ve been told that they are blood sugar related.  Can you share more about these spots?  Will they go away with correcting my food intake?  I’m very new to the GF concept, but I know this is where I need to focus.

  14. Tamra,

    You bring up a great point, and I was thinking of doing a follow-up post on it.  A lot of GF products on the market are highly processed and full of junk.  Just because something is GF, that doesn’t mean it’s healthy.  In a future article on blood sugar and thyroid, I’ll explain why a low-carb diet free of refined carbohydrates (including refined GF carbs) is the best choice for people suffering from thyroid disorders (and everyone else, for that matter.)

  15. Chris, I truly appreciate your insightful articles and your willingness to educate the public about this debilitating auto-immune disease. I have found much resistance (sometimes hostile) among certain Hashi patients who would rather call my dietary changes drastic or crazy. To some people, turning their backs on common sense certainly requires less conviction than bypassing the funnel cake stand.
    I have Hashimoto’s, and when I quit gluten this February, the antibody attacks and swelling stopped. I’ve also cut my thyroid hormone dependence by over 1/4. Now, I only get these attacks when I have a stressful situation or when I eat something that stimulates my TH2 pathways.
    For those Hashis who have tried the GF diet, just remember that eating a piece of yeasty, sugary GF cake every day can be equally as harmful to the gut. I’ve found that cow milk, soy and corn can also cause my gut to swell.
    Hashis must also remember that proper nutrition (especially avoiding processed, fried foods) and exercise is paramount in managing this disease.
    🙂 Tamra

  16. Thanks, Chris. I’m as skeptic as you, after reading a lot of positive stories on iodine group and experience the same with me and my wife (which, by the way, is a m.d.), I can’t believe that iodine could have such a deleterious effect.
    Yes, I have read your series on EFA & fish/fish oil. I was taking fish oil, but stopped and increased sea food (cod, shrimp and crab mostly). It’s so much more tastier!
    Yes, selenium is pretty amazing. It is showed to reduce thyroid antibodies ( and is low in Hashimoto patients (, this study found that hsCRP is considerably lower in persons with high serum selenium!).
    But, make no mistake. Selenium supplementation with iodine deficience is not good (
    Last thing: thank god I don’t live in USA, where bromide levels are the highest in the world. So, make no mistake, don’t underestimate bromide. It is a powerfull endocrine disruptor and iodine + selenium are protective against it (here a study not from Brownstein nor Abraham:

  17. Some other interestings studies about selenium and iodine:

    On your post about iodine, you cited a studies from Brazil, Sri Lanka, Turkey, China, Greece, and Azerbaijan that showed a increase in Hashimoto when iodine was added to salt. The question is: do these countries have a sufficient selenium intake?
    Greece: selenium status is one of the lowest of the Europe (
    Brazil: the study was done in Sao Paulo, city were most brazilian japanese live. Brazilian japanese have significant lower levels of Se than japanese living in Japan (
    China: Minerals as calcium, zinc, selenium, kalium and vitamins as vitamin A, B1, B2 were insufficient (

    Turkey: Selenium status of Turkish children is found to be lower than that found in the literature (
    Turkey: Turkey is one of those countries where iodine deficiency (ID) is widespread, Se levels are marginal (

    Sri Lanka: This study has shown for the first time that significant proportions of the Sri Lankan female population may be Se deficient (
    Azerbaijan: no studies found.

    • Excellent detective work, Mario. After my exam I’ll review these studies and revisit the topic.

      Selenium is pretty amazing. I don’t know if you saw my series on EFAs & fish/fish oil, but selenium completely protects against the effects of mercury in seafood by binding to it and creating a new compound that can’t be utilized by the body. Interesting that it may have a similar effect with iodine.

  18. Chris,
    Thanks, I had already found these papers.
    But, any comment on the study that I linked above, where a high intake of iodine did not cause a immune flare if selenium was taken together?

[if lte IE 8]
[if lte IE 8]