The Thyroid-Gut Connection | Chris Kresser

The Thyroid-Gut Connection


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

Hippocrates said: “All disease begins in the gut.” 2,500 years later we’re just beginning to understand how right he was. And, as I’ll explain in this article, hypothyroidism is no exception. Poor gut health can suppress thyroid function and trigger Hashimoto’s disease, and low thyroid function can lead to an inflamed and leaky gut – as illustrated in the following diagram:


The gut-thyroid-immune connection

Have you ever considered the fact that the contents of the gut are outside the body? The gut is a hollow tube that passes from the mouth to the anus. Anything that goes in the mouth and isn’t digested will pass right out the other end. This is, in fact, one of the most important functions of the gut: to prevent foreign substances from entering the body.

Another important function of the gut is to host 70% of the immune tissue in the body. This portion of the immune system is collectively referred to as GALT, or gut-associated lymphoid tissue. The GALT comprises several types of lymphoid tissues that store immune cells, such as T & B lymphocytes, that carry out attacks and produce antibodies against antigens, molecules recognized by the immune system as potential threats.

Problems occur when either of these protective functions of the gut are compromised. When the intestinal barrier becomes permeable (i.e. “leaky gut syndrome”), large protein molecules escape into the bloodstream. Since these proteins don’t belong outside of the gut, the body mounts an immune response and attacks them. Studies show that these attacks play a role in the development of autoimmune diseases like Hashimoto’s.

We also know that thyroid hormones strongly influence the tight junctions in the stomach and small intestine. These tight junctions are closely associated areas of two cells whose membranes join together to form the impermeable barrier of the gut. T3 and T4 have been shown to protect gut mucosal lining from stress induced ulcer formation. In another study, endoscopic examination of gastric ulcers found low T3, low T4 and abnormal levels of reverse T3.

Likewise, thyrotropin releasing hormone (TRH) and thyroid stimulating hormone (TSH) both influence the development of the GALT. T4 prevents over-expression of intestinal intraepithelial lymphocytes (IEL), which in turn causes inflammation in the gut.

The gut-bacteria-thyroid connection

One little known role of the gut bacteria is to assist in converting inactive T4 into the active form of thyroid hormone, T3. About 20 percent of T4 is converted to T3 in the GI tract, in the forms of T3 sulfate (T3S) and triidothyroacetic acid (T3AC). The conversion of T3S and T3AC into active T3 requires an enzyme called intestinal sulfatase.

Where does intestinal sulfatase come from? You guessed it: healthy gut bacteria. Intestinal dysbiosis, an imbalance between pathogenic and beneficial bacteria in the gut, significantly reduces the conversion of T3S and T3AC to T3. This is one reason why people with poor gut function may have thyroid symptoms but normal lab results.

Inflammation in the gut also reduces T3 by raising cortisol. Cortisol decreases active T3 levels while increasing levels of inactive T3. 1

Studies have also shown that cell walls of intestinal bacteria, called lipopolysaccharides (LPS), negatively effect thyroid metabolism in several ways. LPS:

  • reduce thyroid hormone levels;
  • dull thyroid hormone receptor sites;
  • increase amounts of inactive T3;
  • decrease TSH; and
  • promote autoimmune thyroid disease (AITD).

Other gut-thyroid connections

Hypochlorhydria, or low stomach acid, increases intestinal permeability, inflammation and infection (for more on this, see my series on acid reflux & GERD). Studies have shown a strong association between atrophic body gastritis, a condition related to hypochlorhydria, and autoimmune thyroid disease.

Constipation can impair hormone clearance and cause elevations in estrogen, which in turn raises thyroid-binding globulin (TBG) levels and decreases the amount of free thyroid hormones available to the body. On the other hand, low thyroid function slows transit time, causing constipation and increasing inflammation, infections and malabsorption.

Finally, a sluggish gall bladder interferes with proper liver detoxification and prevents hormones from being cleared from the body, and hypothyroidism impairs GB function by reducing bile flow.

Healing the gut-thyroid axis

All of these connections make it clear that you can’t have a healthy gut without a healthy thyroid, and you can’t have a healthy thyroid without a healthy gut. To restore proper function of the gut-thyroid axis, both must be addressed simultaneously.

Healing the gut is a huge topic that can’t be covered adequately in a few short sentences. But I will say this: the first step is always to figure out what’s causing the gut dysfunction. As we’ve reviewed in this article, low thyroid is one possible cause, but often hypochlorhydria, infections, dysbiosis, food intolerances (especially gluten), stress and other factors play an even more significant role. The second step is to address these factors and remove any potential triggers. The third step is to restore the integrity of the gut barrier. My preferred approach for this last step is the GAPS diet.

The influence of thyroid hormones on the gut is one of many reasons why I recommend that people with persistently high TSH and low T4 and T3 take replacement hormones. Low thyroid hormones make it difficult to heal the gut, and an inflamed and leaky gut contributes to just about every disease there is, including hypothyroidism. Fixing the gut is often the first – and most important – step I take with my patients.

  1. Stockigt, JR and Baverman LE. Update on the Sick Euthyroid Syndrome. Diseases of the Thyroid. Humana Press, Totowa, NJ, 1997, pp.49-68


Join the conversation

  1. Hi and thank you for these wonderful posts. I wish I would have known about them years ago. I had hashimotos and had the raidioactive iodine in 1996, had my gallbladder removed a couple of years after that… I have had severe joint problems, rosacea, exzema, depression and anxiety… and labs have shown B12 deficiency. I also have fibromyalgia with some bad brainfog. I round the GAPS diet and I have been shocked and amazed at how fast I am seeing improvements. I have only been doing this 2 and a half weeks but my skin is much more clear, my memory seems better. My energy level isnt really great yet but my depression is lessening a lot and while I dont have much energy, I am having enthusiasm and at least want to do things now. My question for you is this… I have read multiple things saying that I shouldnt have gone gluten free without a diagnosis first. How important it actually having a diagnosis? I am 50 and supposed to have a colonoscopy as part of a routine checkup and my doctor said that they can test for celiac disease with that. Have i had time to heal up enough and that test wouldnt be accurate? Should I add wheat back into my diet and then do the test. I really hate to do that especially when I read in your article that it can take up to 6 months for this to clear up. While I have only been doing the GAPS diet for a couple of weeks… over a period of months to a year… I have been moving to a diet that had a lot less carbs-which included a lot less wheat. I am fairly convinced that the gluten is what is the issue with me-especially after reading your article and I have so many of these issues but I suppose that there could be something else that I have changed that might account for my improvement. Bone broth or something. I know you cant give individual advice but can you make a general comment on how important or not important actually having the celiac disease diagnosis is… and if people in general should add wheat back into their diet to get a confirming diagnosis or if we should not worry about that and just continue on with what seems to be working.
    Thank you, Sabra

  2. please tell me where to find the complete list of footnote references for this article — only one footnote appears — very interesting article that applies to me totally & I would guess many others — thank you very much!

  3. Hi Chris,
    I am 33 years old, until last 6 months I was fit and healthy.. Suddenly I had a fatigue attack all blood tests revealed normal numbers. Doctors told me may be my low weight is reason and I put on almost 5 kilos in last 6 months or so. I weight around 55 kilograms for height of 5’5″.
    I was running well and had cut down on eating Junk food.
    Residing in India our staple food is Rice, Ragi, Wheat which we cook and have with a curry of vegetables, dal. I am a pure vegeterian no egg or meat in my diet.
    After 3 months I gained some confidence changed diet to add additional small meals to get things going. I felt better started running but with lesser intensity. Past 1month or so I again face similar symptoms of fatigue, sleepiness/tiredness/fatigue through days inspite of eating well and nutritious. So I read about this gut health associated cause related to these symptoms also leading to anxiety/depression. What is best way to come out of it, being in India does GAP diet workout for me since most of nutrition suggestions may be best for Western countries i.e. Eurpope and America? So do you include diet for other countries like India?

  4. I’ve been drinking George’s Aloe Vera water for years and recently was dignosed with Hashimoto’s (antibodies in the 1800’s). Wouldn’t Aloe have any healing affect on any immflamation in the gut?

  5. I just came across this post, which I realize was written a while ago, so no idea if you will see this post or not. But I thought I’d post just in case. Something you wrote captured my attention:

    “Hypochlorhydria, or low stomach acid, increases intestinal permeability, inflammation and infection (for more on this, see my series on acid reflux & GERD). Studies have shown a strong association between atrophic body gastritis, a condition related to hypochlorhydria, and autoimmune thyroid disease.”

    A little history about myself. In 2009, I lost 60 lbs with a low calorie diet. I gained about 15 pounds back last year and this year I have been trying to lose weight. But am having no success. I found if I even eat the amount of calories I should to maintain my weight, I still will end up gaining weight. This led me to wonder about my metabolism.

    My doctor mentioned my thyroid could be the problem and so she had the lab run tests. I have not heard back any results and it’s been about a week. I am assuming a letter will be in the mail saying everything is normal. But I’ve been reading about low thyroid since then and found I have at least a couple of the other symptoms – cold intolerance (I used to be hot all the time and now am always cold) and heavier menstrual cycles. I’ve also read how often tests can come back normal but there is still a problem.

    I also have been having issues with what I assume is either acid reflux/GERD. I spoke with my doctor about this but since it wasn’t happening frequently, she did not find the need for any medication. I was fine with this since I currently take medication for kidney stone prevention and migraine prevention. My husband has been dealing with acid reflux for about 2 years and takes both prescribed prilosec and zantac.

    I actually found your other articles on acid reflux, as well as this article on thyroid. I am interested in learning more about the possible connection of these two things. And any other helpful information/advice you’d be willing to share. Thank you so much!

    • Just wanted to add that I received the letter about my TSH level. It is listed as .73 (with normal range of .4 to 4.5).

  6. Chris, this question is about the GAPS diet, hypothyroidism and all the Cruciferous vegetables the GAPS diet has you eating. Arent these vegetables supposed to be avoided when you have hypothyrodism?

    • Steaming or boiling eliminates a substantial portion of the goitrogens in cruciferous veggies. You don’t need to avoid them, but may want to moderate intake.

        • Fermenting the vegetables makes the goitrogens more potent in my experience.

          It didn’t make me feel sleepy like you would expect but gave me a mild dose of caffeine effect.

  7. Hi,
    My symptoms are
    Pain in left side of abdomen,heavy head,constant fatigue,frequent constipation (with occasional blood in stool),rashes after having nonveg,pain in eye,muscle cramps and irritable behaviour

    Thyroid T3 2.87 T4 0.94 TSH 20.96 ANTI TPO 1300
    AEC 2.08

    Two years ago my stool test showed E Histolytica
    Endocrinologist has suggested thyroid medicine 75mg for life with vitiman supplements

    My questions
    1Could bacteria cause high TSH and allergic symptoms aswell?
    2If not do i have to get AEC and high TSH treated seperately?

  8. Hi from Norway! Lisa truity, I am glad Im not the only one who has experienced that gut health is everything when it comes to thyroid problems (and other health issues). What surprises me is that this approach is not a option when people are diagnosed with low thyroid (at least here). I was given medication (Levaxin) without any further check ups, for example minerals and vitamins, food intolerances or anything else. I live in Norway, and here it is still a “fact” that low thyroid is a life long diagnose and cannot be cured! After reading Dr Peter Osborne’s website (Houston) and his articles on gluten and the connection between leaky gut (which I have obviously had for MANY years), and thyroid problems, I am convinced that this was my problem in the first place, leading to hypothyroidism and fibromyalgi. I discovered I had an iodine deficiency too (had to struggle a bit to get that test done!), and that is also a very important test to do. I have had so many improvments to my health the last 10 months by just eating the right food for me. However, when I tell people (including doctors) that I have cured myself of hypothyrodism, they don’t believe me….. Fibromyalgia is also one of those diagnosis that is “impossible” to cure. Food is everything, and i truely believe that grains are bad for everyone. And the A1 milk we drink here is not a health food either. The “cleaner” my body becomes, the more I react if I without knowing it eat something with grains in it (for example Ester-C vitamins – they contain corn, although it says gluten free on the package). The definition of gluten is not updated in decades. There is gluten in ALL GRAINS, only different types, and I react to all of them, including rice.
    I haven’t heard about berberin – will check it out. You seem to have a lot of choice when it comes to different supplements in the USA. Unfortunately we are not allowed to order supplements from the US, only from other European countries within the EU, though with certain restrictions to how much. We have a very strict law when it comes to medication/supplements here, and the Norwegian equivalent to the FDA thinks that we don’t need supplements as long as we eat a “healty and varied” diet (based on grains and milk!!).

    • Would love to know more about the diet you say cured your Fibromyalgia and Hypothyroidism. I have both and my dr. Just gives me meds and basically says deal with it, there is nothing you can do about it.

  9. I too have been able to reduce/eliminate natural desicated thyroid by improving gut health, eradicating infections. I have had ibs colitis for decades. As a child I had the constipation kind which switched to diarrhea and inflammation. I did the scd/gaps low carb type diets for a few years and coyld avoid the diarrhea, but had gradually developed worsening hypot symptoms as an adult in spite of normal thyroid labs. I had to stay strict with diet or diarrhea would return. I also take zinc, manganese, selenium, chromium, molybdenum, and eat chicken liver pate for iron. This helped energy and libido and caused a slight improvement in thyroid function resulting in a need for less meds on some days. The thing that has really caused me to turn a corner however is berberine and berberine containing barberry root. I started using these alternating about a month ago and they have enabled me to eat normally. Starch and dissacharides no longer give me diarrhea, I have had to drastically cut back on thyroid meds and can envision that I will probably be completely off soon. My mood and energy have increased significantly. Even in the dark dreary winter here in kentucky, I am not feeling depressed. I got the idea to give berberine another try from zhao lipings work on gut infections as a cause for obesity. He mentioned berberine as showing very impressive results in their lab for decreasing bad microbes and increasing beneficial strains in their study subjects. I had some berberine previously but would get bad headaches after taking just one capsule for three days. It seemed like such a small amount I figured I must be having an allergic response. I decided to try again with 1/2 capsule a day and slowly work up. This worked. I guess it was actually die off that caused me to feel bad and berberine is so powerful just one capsule was too much.

  10. So, I have been on a thyroid medicine since 1992, I would love to change my diet and not take the medicine anymore, what do you suggest. I think you are right with it being gut related, burt I have no idea how to start dissecting the issue.

    • I have been on thyroid medicine for more than 15 years. After going Paleo in March last year I had to reduce quite quickly and stopped all medication after 2 months (I got overdose symptoms). When I started medication I had “normal” blood work but had a low FT3. The medication did not do much for me, and I believe that the gluten and casein intlerance I discovered last year is much to blame for all my “low thyroid symptoms” these years. I had constantly gut problems and my diet was low in protein and veggies and fruits and I always had digestive problems. I switched to a Paleo diet over night (no grains, no dairy, no fruits, no soy, no sugar). However, I suddenly experienced a lot of heart burn! It was so bad I thought I had a heart attack! It is possible to get off the medication, it just takes a lot of hard work and strong will. I had strong withdrawal symptoms for 3 months and at first I thought I was going to die (!); I had a hard time breathing, I was dizzy and even got ME symptoms for a few weeks (could not read, watch TV, etc). I guess my body was exhausted from being fed the wrong food for such a long time (decades). After 8 months into the new diet I found out I had a bacteria infection and yeast. I also had iodine deficiancy, as well as zink, magnesium and iron deficiancy. It takes time to heal, but if you change your diet it will affect your medication quite fast, maybe after a couple of weeks. So listen to what your body tells you, but at the same time be prepared there will be withdrawal symptoms. I have been without medication for 8 months now, and I no longer have all those symptoms I had when I was taking medication for low thyroid and my FT3 has never been better than now. My recommendation is that you take it very slowly, step by step. It is possible!

    • Connie, my suggestions would be that you get tested for food intolerances (IgG a good place to start) – preferably before you get off grains and dairy. If you change your diet to grains and dairy free, be sure you will get withdrawal symptomes… I had tem for 3 months. And please be aware that your medication will probably have to be reduced as you go along. I had to start reducing Levaxin after 2 weeks on the new diet. You can of course also take a week by week approach, and sort of adapt to a new diet over some time, and eliminate dairy first and grains afterward.
      A stool test is the best thing I have ever done for myself – as it turned out I had bad bacteria and yeast (I took one called CDSA 2.0, one of the best there is, I think). The Lab is Genova Diagnostics (Asheville, NC). You need good bacteria for your gut anyway, and these capsules can be bought wthout prescription. I use them every day. Try also digestive enzymes to your meals (lipase, amylase, protease) and see if that helps on digestion. They are also without prescription (at least here in Norway). I would also take omega 3, 2 table spoons olive a day oil and start cooking with coconut oil. All other oils should be banned. Coconut oil is good for the thyroid. I would also do a 24-hr urin test to make sure you have enough iodine. You also need to check your mineral and vitamins, especially vit D, magnesium, zink and selenium. If you have a leaky gut you probably have deficiencies in these minerals and vitamins (I did). Start with 1000 mg C every day (make sure they are without grain/soy based ingredients).
      Listen to your body, but reaslize that there is no quick fix to a gut/health that has been compromised for many years. I am still not “there”, after 10 months, and one problem I still have is eating fruit. My stomach starts WW3 everytime I try a banana or a handful of berries. If anyone out there has expereinced the same, I would appreciate hearing from you!
      Don’t care about friends and family caling you a nut case because you stop eating grains..or dairy! Good luck from Norway!

  11. Chris, with your recommendation of ginseng for supporting the cortisol rhythm, does it matter whether one is TH1 or TH2 dominatant. In reading Dr. K’s book that was the thing that was the most confusing. Without access to the tests or practictioners I wouldn’t want to treat the wrong one.

    Given that it is a rhytmic thing, should the ginseng be taken at certain times of day?

  12. Along with the GAPS diet for gut heaing we need to include colon cleanses either with thereputic enemas or colonic hydrotherapy sessions.
    Blessed Herbs has a complete herb cleansing kit.
    Also Kristina Amelong’s book, Ten Days to Optimal Health gives great advice on cleansing, detox, gut healing, colonics, etc.  She also has a website to purchase at home enema kits and detox supplements (cheaper then Blessed Herbs): She recommends bone broths and raw milk while cleansing, whereas Blessed Herbs recommends fresh pressed juices like apple juice (not possible for those with blood sugar problems).
    Their colon cleanse supplements are basically the same: bentonite clay, pysillum husk, apple pectin.
    If you have blood suagr problems, it may make cleansing more difficult.  I used True Balance supplement as suggested by Julia Ross in the Diet Cure to help and followed the raw milk and bone broth plan.  Amelong also recommends flax oil and coconut oil while cleansing.
    I find this approach to work and is so much easier to do than GAPS alone (the extra fiber is filling) with faster results.  I believe The GAPS diet also reccomends enemas and/or colonics, but only briefly and does not go into great detail about it.
    It is recommend that a person does 3-4 intense cleanses a year for one to two years if in poor health.

    • I’m not a fan of colon cleansing. Colonics can be harsh and depleting, and I don’t think they’re necessary – especially on a repeated basis. I can see a role for enemas over a short period, as Natasha suggests for people following GAPS, but I don’t recommend either colonics or enemas over an extended period. This is particularly true for people who are debilitated and have sensitive guts.

      • Colonics are invaluable. After fasting for 8 days, I had one done and there was morbid matter released every time. Days 9 and 10 were the same. I had another one on my last day, day 28, and got the same results. The same can be said for the day 29 and 30 when I had yet to consume anything solid. That was pure morbid matter stuck in my intestines. Not only did I feel refreshed, but hardly depleted. Even if that was the case, feeling depleted pales in comparison to the benefits of clearing out the decay from the colon.

        Dr. Walter Crinnion, ND, is world leading expert in the field of environmental medicine. His success rates implementing colonics in many of his patients has also been invaluable.

            • The summation of a parasite diagnosis by Bonnie may have to do with the metabolites produced by parasites either in the presence or absence of food. I have no sources but my boss has battled with parasites & has explained the effects of the metabolites on different parts of the body.

  13. It can be a genetic condition, but as I’ve written in my articles it can also be caused by inflammation, stress and high homocysteine levels.  See #5 in this article, and reason #2 in this article.

  14. Still a little confused over here. Do you consider thyroid hormone resistance to be an autoimmune condition? Can’t seem to find it in your previous articles.

  15. I’m not a big fan of the gland supplements.  A more sophisticated approach is to use adaptogenic botanicals like Panax ginseng, Siberian ginseng, Ashwagandha, etc. that elevate or reduce cortisol as necessary.  The most important thing is regulating the cortisol rhythm. You can have normal levels of cortisol, but if the rhythm is off, you’ll have symptoms.

    • Ashwagandha irritates the gut and many people with gut issues have side effects with it. Some of which include allergic reactions.

  16. Thanks, that clears up a lot and I’m looking forward to your next post! You say that the way to go is with a compound that regulates the cortisol rhythm, is adrenal gland tablets (in Sweden called Adrekomp and containing extract from natural adrenal glands from pigs along with vitamins A, C, B1, B5 and B6, minerals P, K, Zn and Betain HCl) such a compound?

  17. Another higly interesting post and yet I feel slightly more confused by every post I read, it’s a lot to take in and I guess the language barrier doesn’t help. I don’t know if I’ve got it all right and if I’ve missed something but I can’t understand that cortisol would decrease active T3. I’ve been recommended to support my adrenal glands by taking cortisone or a natural supplement with adrenal gland extract. I chose the latter and it’s helped me a lot, I feel much better. Now with what you’re saying about T3 it seems like it should’ve had the opposite effect? And what is your take on adrenal gland fatigue? The more I read (not only here) the more I think that my thyroid problems actually are adrenal glands problems. And finally, you haven’t really said anything about hypo2, I presume you’re familiar with Dr Mark Starrs theories. How do they fit in with your take on it all?

    • Charlotta,

      Many of your questions will be answered in my next article on adrenal stress and the thyroid, which I will publish either today or tomorrow. I’ve read about Type 2 hypothyroidism. I have been talking about it, but not under that name. Whenever I say “thyroid hormone resistance” or “thyroid receptor site downregulation”, that’s what I’m talking about. Cortisol depresses thyroid functions by several different mechanisms, which I’ll outline in the next article. Taking cortisone is not the way to support your adrenal glands. Taking compounds that regulate the cortisol rhythm is.

  18. Superb post Chris!
    What do you think about the possible effect of eating charred meat on serum AGEs, and on health in general, in people with a health GI tract.
    Here is the reason for my question. I had a few exchanges with a commenter under the post below. I looked into some refs the commenter provided.
    It seems that, in the absence of gut problems, ingested AGEs (e.g., Maillard) may not be a big deal. But I’m not sure.

    • Ned, you’ve looked into the AGE issue in much more depth than I have. The conclusion I reached after the little bit of research I did was similar to your own: that the potential damage caused by AGEs – even when someone has a leaky gut – pales in comparison to the harm caused by refined carbs and industrial seed oils. Based on the evidence I’ve seen, I don’t find cause to strictly avoid roasted or BBQ’d meat, but at the same time I wouldn’t eat it every day. For me this is a quality of life issue as well. I am interested in health, of course, but I’m also interested in living well. The pleasure that eating a particular food and the real physiological benefit that pleasure brings is always a part of the equation.

  19. While having no familiarity with thyroid issues, I’d still be interested to hear your (possibly relevant) take on the health of the “second brain,” something my tai chi teacher wrote about and which “Scientific American” and the NYT has covered. Many believe that traditional fermented foods are smart choices for promoting healthy intestinal flora, e.g. “the Activia Challenge.”


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