The thyroid-gut connection

July 29, 2010 in Thyroid Disorders | 13 comments

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


Hap July 29, 2010 at 11:48 am

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.”

Chris Kresser July 29, 2010 at 5:04 pm

I read Gershon’s book The Second Brain several years ago and was fascinated by it.  I’ll have more to say about this in future articles.

Ned Kock July 30, 2010 at 8:42 am

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.

Chris Kresser July 30, 2010 at 10:09 am

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.

Charlotta (Sweden) August 1, 2010 at 6:50 am

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?

Chris Kresser August 1, 2010 at 8:22 am


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.

Charlotta (Sweden) August 1, 2010 at 8:47 am

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?

Chris Kresser August 1, 2010 at 9:39 am

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.

Charlotta (Sweden) August 2, 2010 at 5:11 am

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.

Chris Kresser August 2, 2010 at 8:39 am

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.

Lg August 2, 2010 at 2:03 pm

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.

Chris Kresser August 2, 2010 at 2:29 pm

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.

Phoenix August 3, 2010 at 4:30 pm

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?

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