Thyroid Hormones and the Gut


Poor gut health can impact thyroid function and be a factor in the start of Hashimoto’s thyroiditis. Conversely, it is well known that poor thyroid hormone levels can lead to gut problems like bloating, inflammation and leaky gut. An old Greek guy called Hippocrates is famous for saying "all disease begins in the gut"... maybe he was right.

The Gut has Multiple Functions

It is designed to prevent substances that we are not meant to digest from getting inside our bloodstream and to the rest of the body.

The gut is a host to 70% of our immune system tissue. This part of our immune system is called GALT (gut-associated lymphoid tissue). The GALT is made up from: 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 dangerous.

The gut is also the host of up to 2-3 kg of hard working bacteria and yeast, the very important intestinal flora. The ideal is to have a gut flora dominated by healthy bacteria and yeast and not an overgrowth of harmful ones, like candida, clostridia and many others. The harmful pathogens, like candida, also do useful jobs too like the good ones. They can clear some waste from the body, but in an overgrowth they cause a lot of damage and weaken our whole system. A harmful over growth of one of these pathogens will weaken our ability to break down and digest food, absorb nutrients and clear the waste and toxins like viruses and others. An imbalance between the good gut flora and the harmful pathogens is also know as dysbiosis.

A healthy gut flora can help the body manage both mercury and parasites many times better than a poor gut flora with an overgrowth of pathogens. Apart from protecting us from infections it protects us from carcinogenic and toxic substances by neutralizing them, taking care of them by holding them tight and transporting them out of our body. A study looked at two groups of animals where one was treated with antibiotics and another served as control. They were given huge amounts of organic mercury and among the animals not treated with antibiotics (who had a healthy strong gut flora), only one percent of that mercury managed to get into the body from the digestive tract. In animals treated by antibiotics that wiped out their beneficial gut flora, about 95 percent of the mercury got into their body and their blood stream and bones, muscles and everywhere else.


An overgrowth of pathogens will attack the intestinal wall, break down the villi (the cells that are supposed to take care of digesting food), pierce it (especially clostridia with it’s spiral shape) and create gaps in it. The lack of villi and these gaps will turn starchy and processed food into toxins, since the food is not being correctly digested by the intestinal wall. Some of these toxins can pass straight through the gut wall, enter the bloodstream and then spread throughout the body. This is known as leaky-gut syndrome. The body will see these toxins it as enemy substances and feel attacked. The non-digested food will stay in the intestines and get fermented. That fermentation will feed the pathogens further and they will increase even more in a vicious circle. The digestion of the pathogens creates gases that are toxic and will weaken our detox system. Other toxins that we are exposed to will be more difficult to deal with.

Poor Gut Integrity and Autoimmune Diseases like Hashimoto's Thyroiditis

So, when the gut becomes permeable, as in leaky-gut, proteins that are not broken down sufficiently or ones that should not be absorbed at all may leak through the gut lining and into the bloodstream. When this happens the immune system senses them as substances that should not be there and attempts to attack them. Research has shown that this is a likely mechanism in the development of autoimmune diseases like Hashimoto's thyroiditis. Gluten that is contained in grains like wheat is often implicated in damage to the lining of the gut. Hence, going gluten-free is often recommended as a key strategy when dealing with Hashimoto's thyroiditis. Dr Natasha Campbell McBride (the author of the GAPS book - 'Gut and Psychology Syndrome') even suggests that it is necessary to cut all starchy food, not only gluten, since a compromised gut flora will not be able to digest it and it will cause damage.

The Gut and Thyroid Hormones

Good thyroid hormone levels have been shown to protect the gut lining. In studies of gastric ulcers low FT3, FT4 levels have been found and high levels of rT3 have been detected.

The gut is also involved in converting FT4 into FT3 locally within its tissues. Around 20% of the FT4 converted to FT3 in the body takes place in the gut.


Intestinal dysbiosis may be described as being an imbalance between the good and bad (pathogenic) bacteria in the gut. Dysbiosis reduces the conversion of thyroid hormone into the biologically active T3. In addition to this, inflammation that arises out of dysbiosis creates more demand for cortisol, which is needed to dampen down the inflammation. Increased cortisol impacts on thyroid hormone action and can raise rT3 levels and decrease FT3 levels. There are also studies that show that the cell walls of some pathogenic bacteria can affect thyroid hormones by reducing active levels of FT3, blocking thyroid receptors, increasing rT3, decreasing TSH and helping to create the conditions for Hashimoto's thyroiditis.

Low Stomach Acid and Slow Gut Transit

Low thyroid hormone is also known to reduce stomach acid levels. Low stomach acid (hypochlorhydria) in turn allows more bad bacteria to flourish, increases gut permeability and inflammation. Since protein will not be broken down with a lack of stomach acid it will create constipation and that in turn will cause toxins to develop when it is not cleared from the body within at least a couple of days fermenting. There are connections between gastritis and autoimmune conditions. Low thyroid hormone often causes the gut to slow down and this can impair the clearance of hormones like oestrogen, which can also impact thyroid hormone action further. Constipation will also increase inflammation and the risk of further bacteria imbalance and poor absorption of nutrients.

What to Do About The Gut?

To have a healthy gut you need good levels of thyroid hormones and especially the biologically active thyroid hormone T3. You also won't get thyroid hormone action to be effective without a healthy gut. There are too many connections between thyroid hormone effectiveness and a healthy gut for only one of these to be a focus. Both the gut and the thyroid hormones must be focused on if there are problems in both.

It can also be hard to see which is the chicken and which the egg? Is it a thyroid hormone issue, leading to gut issues in an individual? Is it a gut imbalance leading to worsening of thyroid hormones. Anecdotally, I had many gut symptoms when I was on T4-Only therapy. When I eventually was given T3-Only, these all vanished in a few weeks! But everyone has their own specific issues.

Healing the gut is beyond the scope of this article and well outside my main sphere of interest. However, experts suggest that one of the first steps should be to figure out what’s causing the gut dysfunction. Low thyroid hormone is one possible issue, low stomach acid, infections, dysbiosis, food intolerances (especially gluten and other starchy and processed food), stress and other factors may be part of the problem. Dietary change, probiotics, detoxing, removal of other dietary or lifestyle triggers may be required.

Low stomach acid is very common and should be considered when thyroid patients have digestive system issues. There are many approaches that may be used with hypochlorhydria including the use of betaine hydrochloride with pepsin. Dietary changes such as going gluten and dairy free, the Paleo diet or the GAPS diet may also be considered when someone wants to restore the integrity of the gut barrier.

Final Thoughts

I hope this brief foray into Gut and Thyroid connections may have given some readers some ideas that they can translate into something useful for them.

A couple more final points are worth mentioning. Firstly, a person with gut integrity issues does not necessarily have obvious digestive system symptoms. The problems can be there and can be impacting the immune system and other aspects of the person's health. Those people that have no obvious digestive system issues often feel that focusing on the health of their gut and dietary changes that support this will not help them because they have no symptoms - this is not necessarily true. Secondly, thyroid disease is often a disease of the immune system at heart rather than a disease of the thyroid gland, so working on healing the gut and then maintaining its health is often key to long term recovery and good health. I do not focus on the gut as it is not my area of value-added expertise but once in a while I have to mention it as it is so important.

There are a few books that I'd like to suggest are really worth reading:

1. Hashimoto's Thyroiditis by Izabella Wentz
2  Gut and Psychology Syndrome (GAPS) by Dr Natasha Campbell-McBride
3. The Paleo Thyroid Solution by Elle Russ
4. Practical Paleo by Diane Sanfilippo (there are many other good Paleo books also)

Best wishes,


(Updated in February 2019)