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. I ran across this late in the game, so I’m sure you must have an article to address this and if so, I’d appreciate a link. So given what you addressed, does it then make sense that some of us experience chronic diarrhea while in fact suffering from hypothyroidism? That is my situation. The diarrhea is a result of an autoimmune response to leaky gut, which in turn produces low thyroid function? Is that what you are saying?

  2. Love this post! I found it when, after starting on bone broth, I had to immediately (within days) reduce my T3 medication by almost half (T3 only – 62.5mcg to 37.5mcg). I thought I was having a Hashimoto’s induced hyper spell, but my pulse and temps have remained stable, even while reducing the T3. I can hardly believe this is possible! I thought I had healed my gut by cutting out all gluten, grains, dairy, and soy, as well as adding in fish and eggs (I had previously been vegan) and lots of ACV in my water daily, but over two years of this and I’ve been stable at “feeling okay.” Now a few weeks of bone broth and I’ve cut my meds, have more energy, and am slowly losing weight (just a couple of pounds so far, but the right direction). Am I kidding myself here? Could this be attributed to something else? Again, thank you for this and all of your other, very helpful and informed articles.

    • Rachel, I too am hypothyroid and trying everything I can to eat what is healthy for me to “heal” myself of hypothyroidism. I too have started bone broth after reading about all the good it does for people with our condition. I would love to know more about your bone broth experience and how and what else you are doing to get well. I’m thrilled to hear people are actually getting better. Is there a way I can contact you directly?

  3. Hi Chris,
    I’ve read a few articles and rather enjoy them. This one hits home. My girlfriend has hypothyroidism and is trying to lose weight. She has lost a significant amount but did it very unhealthly, barely eating and lots of running. I am an exercise physiologist by trade and we started working together. When we met I had to fight with her to eat more than 1200 calories. We’ve slowlly worked up to her normal resting metabolism (1700kcal via medgraphics indirect calorimetry). However, she is extremely bloated, added 8 lbs to the scale (while starting to train for an endurance race). Her blood tests recently came back all clear but her digestive tract is virtually not working. 5+ days without a movement, undigested food, feelings of constipation etc etc. Her mensi’s is off as well. I think the link is between her GI tract and Mensi’s. Any idea? She’s on synthroid and very active, 4 cardio workouts and 4 weight training sessions. I am at a loss.

    • I used to be just like that. There are other meds much better than Synthroid. She should go to, read there, and find a “good doc” and get checked out. I did after being on Synthroid for 10+ years, gaining weight yet working out like mad. I am now on Naturethroid for 2+ years and feel much better. Finding a “good doc” is the most important. I hope this helps.

  4. Two days ago i woke up feeling weak and out of it. Took my temperature. It was 93.8. I asked the doctor to take a blood test and my TSH came back at .7. Two months earlier it was 1.0. I’ve been under constant stress for the last three months, not sleeping much, and very agitated. More recently I’ve been very constipated, not peeing much, always hoarse, night sweats, foggy thinking. I suspect with all my agita I may have done a number on my pituitary causing it to stop sending TSH to my thyroid and giving me hypothyroid symptoms. If I am right, is there anything I can do to get my pituitary back to sending proper TSH to the thyroid?

  5. Hi Chris,

    I’m a 40 year old female with a previously active lifestyle. I had a slew of crazy health issues earlier this year– weight gain (25lb in 6 months), fatigue, body aches, GERD, depression, Brian fog, muscle cramps, heavy and horrible periods, PMS, etc. I was convinced that I had hypothyroidism, but all tests looked “normal” except for a lower FT3 and an RT3/FT3 ratio of 18 (pointing to cellular hypo?). I had torn a shoulder muscle the year before and was popping Advil and muscle relaxers all the time. I also had strep throat 6 times that year as well as a UTI and had taken antibiotics each time. I could not catch a break! I ended up going to a integrative MD after the heartburn and stomach pain was beyond what OTC antacids could handle. he ran a stool and blood allergy test. Turns out I had an H. Pylori infection and an unknown parasite– most likely all the Rx’s and Advil created the perfect breeding ground for that to happen. I was given more antibiotics to treat the infection (I wouldn’t if I knew there was an alternative) as well as progesterone cream for estrogen dominance. Things seemed to get better for a short time, but now I have 18 food allergies brought on from leaky gut and I’m still tired and depressed by my lack of energy. I can’t lose the weight no matter what I try– it won’t budge. I’ve cut wheat, whey/casein, eggs (I’m allergic to them all now) and just this last month I’ve cut alcohol completely. Still, no progress! Now I’m doing acupuncture and a series of cleanses. What else should I be trying??? I’m still not convinced that my thyroid is okay, but my dr has kind of thrown up his hands.

  6. Chris,

    Thanks for the great website.

    I was diagnosed with Ulcerative Colitis over 12 years ago. Recently I discovered that there may be a real connection to my adrenals. During an appointment with my endocrinologist, he found a large (benign) nodule on my thyroid. So, all the medicine (ASACOL) I’ve been taking for 12 years may not have been addressing the root cause of my condition. I have a good endocrinologist and will be focusing on my adrenals and thyroid once I am tapered off Prednisone.

    Do you have any resources that confirm the connections between UC, the adrenals and thyroid?

    Thanks again. Knowledge is hope.

    Scottsdale, AZ

  7. I followed the link to the GAPS diet, and agree with a great deal of the information contained therein. Probiotics, carrot juice, essential fats, etc….

    Can you contrast the diet itself with a vegetarian diet? I am a vegetarian with low thyroid and am on HRT (androgel).

    I avoid gluten, supplement with whey protein, and exercise vigorously 5 days a week. Even with this routine, I still struggle to lose weight.

    Thanks Chris, awesome information you bring!

    (I’m 49)

  8. Thanks so much for this! I just found your website. After suffering immensely for the past 15 years with Hashimoto’s, and probably to some extent since my early adolescence, I am finally on GAPS. My daughter, who just turned 15, is starting to suffer from the same symptoms I have had. Now I can help her to break the cycle of disease and live a better life than I have been able to. It is so important that you, and doctors like you, are doing more than just prescribing a pill, and trying to discover the cause of disease. So often I have wondered, “Why me?” Now I begin to have a glimmer of understanding. Thank you!!!

  9. I’ve been on GAPS for about a year now and only recently have found alot of people saying that they have gotten Thyroid issues from being on GAPS and I’ve done research that says that we need some carbs other then veggies! So is its really harmful to stay off grains and starches? As I feel better staying off them and was going to permanently.

  10. Hi There,

    I was wondering if you could recommend good MDs that have an alternative approach or GAPS background who are in the SF Bay area. I am having really bad gallbladder( GB) issues with no relief. Seen docs for the past two years about my GB and they all wanna yank it out. I am not overweight, 34 female and have been on Paleo but yes not diligently which is the problem. If you know of any please let me know… I am searching around myself and appreciate any ideas to start my real healing.

  11. Hi, I’ve been suffering from the following symptoms: chronic constipation, cold intolerance, and a very low immune system making me very susceptible to infections. My magnesium levels are in range but consistently over the past year my lymphocytes and immune system is in the lower borderline( 850-3900). MY TSH and T3 levels are also low, especially my TSH which is significantly low. Please advise me how I can treat this ? I always eat very healthy ( no gluten, no dairy,) and exercise and try to minimize stress.

  12. I started having problems about 7 years ago, right after my mother passed away and I started pre-menopause. I had such heavy bleeding that it caused anemia. My gyn at the time tried me on several heavy pills that caused my whole body to go out of whack. Long story short…I felt like I was having thyroid & hormonal issues. As for the thyroid, no one would put me on any thyroid meds (until now…too late in my book!) I developed 3 nodules. They continued to grow. I had just about every symptom of hypothyroidism..some sevearly. I developed MS. I went to a neurologist and described all of my symptoms and he sent me to an endochrinologist. This dr. finally put me on synthroid. It was like a miracle. All the things that I had been complaining about went away. For about 6 months that is! I got a sinus infection and had to go on antibiotics. For some reason the antibiotics also had potassium in them, for which I cannot take (IC), so I stopped them about 2 days shy of the dose. A few days later I began having terrible digestion issues. I have had slight IBS before in my life, but nothing like this. Severe bloating, gas, pelvic pain, distension, weight gain (23 lbs in 3 months), water retention. Burping even when drinking water. My endo switched me to Armour, but reduced my dose. My nodules were still growing, so he recommended I have my R side removed, which I did 2 months ago. They would not raise my armour and said my TSH is slightly high. I am still having terrible digestion problems, weight gain, etc. My other levels are all normal, except for my cholesterol is high. I am at my whits end!!!!! Now they say to take estrogen. I do have a history of thyroid disorder (mother). I read not to take estrogen, so now I don’t know what to do. I am now on gluten free diet, whole/clean foods, but only a slight change. I take probiotics and Keifer daily. I really don’t know where to go from here. No one will give me more armour to see if it helps.

    • Linda,

      I posted the above question to Chris (I’m a different Chris) .

      I’ve been through much of what you describe. And, I have a suggestion or two. First, I use both Armour/Synthroid. I’m truly useless without the T3 from Armour. The only way my body functions properly is if my TSH is driven down into the 0.0something range, Period! Higher and I have all the classic hypo symptoms.

      Second. I was having a horrible prob with bloated belly, constipation, and so on. Even with regular exercise and strict diet. It was inflammation. What worked was a water fast for 10 days. Then months of fat free, low cal Atkins to get myself (as fast as possible) to my ideal weight. Then lifting weights at the gym 4x/week.

      Is it a cure? Nope. Did it fix my symptoms? Yes! It might not be what you wanted to hear. But inflammation is a monster and left uncontrolled, it ruins your life. I had to take drastic action. And, am I glad I did!

      I now know that I cannot eat anything man made (short of zero carb whey protein after a workout) And, I mean nothing. No man made salad dressing, no bread, crackers, pasta, no cooked veggies, no processed anything. Just smoked fish (in my electric smoker) chix, a touch of lean beef and turkey. Plus dried meats. The reason for this is clear. My body attacks carbs of any sort. Driving insulin levels up, storing it as fat and causing inflammation. There is a clear relationship between stored fat and inflammation. Get rid of it, period! There is a clear relationship between inflammation and all these symptoms. I’d much rather have fewer symptoms, wouldn’t you?

  13. I have Been dealing with thyroid issues all f my life. I am 26 and have within the last year figured out sometbing is really wrong with the way I feel. What should be my first step in fixing my thyroid issues. Should I get a blood panel test to see where my levels are and how it’s affecting my hormones or should I go straight to gaps diet? I am big on traditional gods and have started takin fermented cod liver oil, gelatin, coconu oil, grass fed butter and prescript assist probiotics. Also have been brewing kombucha for my gut health. I still feel my blood sugar levels dropping and I get really sick and weak. I feel so miserable like I am dying! I hate it and I’ve had enough!! Please let me know what I should do first.

    • Why haven’t you tried progesterone cream? Or ask your GP for an Rx for Prometrium. It will fix your low sugar s it did for me sounds like you are estrogen dominant. Skip the ferments they make things worse.

  14. Hi,

    It is important for me to thank you for this very interesting site. It gave me explanation to the mystery of my healt problems I am searching for so long! When I was around 16, I started to loose lots of hair and feel cold all the time. At 18, on one extremely ordinary morning, I started to feel extremely cold, anxious, depressed and I started to fall asleep almost anywhere. I always told the doctors that those symptoms were all related but as my thyroid gland exam seemed normal, they just insisted to give me medication for every symptoms (ritalin (for narcolepsy), Paxil, psychologist referral to find imaginary traumas, anti acid for the stomach -nexium…). Everything just went worst and I am 37 now and decided to make my own research and saw the Gapsme site (have lots of digestion problems since childhood) and then I saw your site. I have started a anti candida (have lots of symptoms for that as well!) diet. I red that thyroid problem can often be undetected with the classical test. Because of the normal result exam, doctors refuse to give me the thyroid classical medication and I am now followed by a nathuropath for the bad gut condition. I have always been convinced that there was something wrong with my thyroïd even though doctors are almost laughing at me and deny any relation in my symptoms. Is there natural substances that I can take to help my body produce the thyroid hormones? Is there any substances that does not need a doctors prescription that would help?

    Thanks again for your website, it is extremely useful- a revelation for me! Marie-Eve

  15. My daughter is GF but not dairy free. We do not worry about cross-contamination, so I can see where we could improve our concerns there. Anyway…she has AIT, but the hyperthyroid type. She is only 8 and so far no palpably enlarged thyroid nor eye involvement. Because she is young, we are not interested in “killing” her thyroid and putting her on thyroid meds the rest of her life. We have been doing biomedical treatments since 2010 so we have been on and off probiotics with no known “visual” benefits, but being that she is 8, I am not sure I would notice (she has never been one to complain of body pain)

    Well, my question is, is there a probiotic you would recommend for her, specific to AIT/hyperthyroid/Graves? I am not exactly looking to improve t4 to t3 conversion LOL unless there is a specific probie that will prevent reverse t3.

    Her other existing issues are: recovering from ASD, anxiety, sound sensitivity, positive thru DD labs for C. Diff and GPL labs indicating dysbiosis (treated on and off with high dose probies, like VSL#3 and Custom Probiotics)

    Thank you for any suggestions. 🙂

  16. Very fascinating! I developed hypothyroidism several years ago, when I made the mistake of going on birth control. I have gotten smarter since, came off it, changed my diet, reversed hypothyroidism, but always wondered what damage I might have done long-term to my gut flora. I recently spoke with a specialist who suggested doing a probiotic treatment (a month for every year of birth control use) to restore balance. As I am getting ready to do it ASAP. Meanwhile it made me wonder if thyroid issues and gut health have a lot in common–glad I found your article to confirm my hunch.

    • Hi Elena, it seems that we had similar reactions to birth control pills, would you be willing to email me about what you did to get to where you are now?

  17. So, what does a person who has no thyroid do? Mine was removed 7 yrs ago due to thyroid cancer. I take thyroid meds but still feel yuky and have constipation and digestive issues…all the time.

    • Stop the thyroid madness has a website and book

      Or Adrenal fatigue 21st century has a book

      If you have these two and your asking this question then couldn’t help you however if you don’t they are well worthy investments

  18. Hi Chris, very interesting and informative site, thanks! I hope you’ll take a minute to answer a couple of questions. I’m 49, male w/hashi’s (since age 33) , taking 75syn and 90 armour/daily. On a lower dose, my labs come out perfect but I feel awful and have all the problems you list, including major fatigue, near constant low blood sugar, significant intestinal blockage, rock hard bloated belly and major joint pain. On the higher dose listed above, I feel well enough and those problems fade nearly completely. I’m on a strict low carb diet (by necessity) and not diabetic. I also am an avid bicyclist and ride about 100 miles per week. My 2 questions are: First ( #1) when I work outside in the sun and modest heat, in short order I get very low blood sugar, below 70, regardless of type or quantity of food intake, candy does not help. Only time fixes it. Second ( #2) I now have tingling feet and hands, which I am now understanding can be a symptom of hashi’s. Is there anything I can do to improve these conditions?

  19. I have graves and had my thyroid removed two years ago. I’m trying to address my thyroid related food issues now, but am unsure how to maintain proper nutrition while respecting my food sensitivities (beef, eggs, lamb, tree nuts, dairy and gluten) while breastfeeding. My 9 week old son is very fussy and I’m wondering if I eliminate my food sensitivities would this help him? Also since I feel pretty limited on hat I can even eat how do I ensure my dietary changes don’t affect my milk supply? Lastly, since I no longer have a thyroid am I will considered a Graves’ disease patient or do I now have something else? Thanks!!

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