The Thyroid Gut Connection + 4 Steps to Heal Your Gut

Dr. Jolene BrightenPublished: Last Reviewed: Thyroid & Hormone Balance Leave a Comment

Chances are if you’ve made a trip to your endocrinologist for your hypothyroidism you’ve heard that your condition is genetic, there’s a prescription for it, and that’s about all you can do. It's an autoimmune thyroid disease. Period. I’d even venture to guess that there was no mention of your gut health at all…let alone the thyroid gut connection. What is gut health, what is a leaky gut? These are all questions you may have.

And why would your endocrinologist talk to you about your gut? In the conventional medicine paradigm, the endocrinologist’s job is to care for your hormones, while the gastroenterologist cares for your gut. But I’m here to tell you that they are connected and you must address both if you are to restore the function of your thyroid.

About 20% of thyroid hormone conversion takes place in the gut. Click To Tweet

Leaky Gut and Hypothyroidism

Hashimoto’s, or autoimmune thyroid, is the number one cause of hypothyroidism in the United States. And while not all causes of hypothyroidism are well understood, we do know that if you have an autoimmune condition, then your immune system is not behaving as it should.

And where is the majority of your immune system located? Your gut!

It has been estimated that your gut houses anywhere from 70-80% of your immune system. This aspect of the immune system, known as the gut associated lymphoid tissue (GALT), can become triggered by infectious agents, food particles, and other proteins that make their way through the lining of the intestine in a condition known as “leaky gut.” Exposure to these “non-self” proteins or antigens stimulates the immune system to produce antibodies.

The job of antibodies is to tag foreign proteins for destruction. However, in the case of molecular mimicry, the amino acid sequence of the non-self protein that has been tagged for destruction closely resembles an amino acid sequence of self proteins, aka your body tissues. When this happens, your immune system can mistake your tissues as foreign and begin to attack the target tissue, in addition to causing inflammation in the body.

The job of the gut mucosa or intestinal lining is to allow nutrients to pass through for absorption and utilization in the body. At the same time, the intestinal lining should keep harmful proteins from entering. But in cases of leaky gut, these proteins are able to cross this protective barrier and trigger an inflammatory response.

Over time, after repeat exposure, the body will respond by creating antibodies, which can set off a cascade of autoimmune destruction of the thyroid tissue — resulting in Hashimoto’s and eventually hypothyroidism.

Download your FREE Hormone Starter Kit with Recipes to Heal Your Gut and learn more about how optimizing thyroid health

Potential Causes of Leaky Gut:


Long-term, regular  use of NSAIDs (non-steroidal anti-inflammatory drugs) like ibuprofen can cause damage to the intestinal lining.

Birth Control Pill.

Birth Control Pills are one of the most common medications women take that can contribute to leaky gut. The pill induces inflammation and leaky gut within the intestines and increases the risk of autoimmune disease. Read more about in this article: Is Birth Control Bad for Your Gut?

Antibiotic Use. 

Antibiotics disrupt the normal healthy bacteria in your gut and leave it susceptible to harmful organism overgrowth.

Mom’s exposure to antibiotic due to C-section or Group B Strep will cause disruption of both mom and baby’s gut. Antibiotic use in general can disrupt intestinal flora and gut lining for 6-12 months.

Chronic Stress. 

Stressors from work, life, and even exercise or strict dieting can alter your microbiome and lead to leaky gut.

High Sugar Diets. 

Diets high in processed grains and sugars can lead to damaging hormonal swings, not to mention feed yeast, bad bacteria, and pathogens in the gut. There are so many reasons to cut down on the sugar.

Low Fiber Diets. 

Diets rich in fiber, both soluble and insoluble, have been shown to reduce the risk of developing many gut pathologies, including leaky gut.

The Thyroid Gut Connection

“But I don’t have any gut issues,” you may be thinking. Alas, It is possible to have food sensitivities, dysbiosis, and other gut conditions – even Celiac disease! – without any overt gut symptoms at all. In fact, estimates indicate that the majority of people newly diagnosed with Celiac disease do not present with gastrointestinal symptoms. In many adults, neurological symptoms are often the first sign of Celiac disease.

Other gut conditions can present with rashes, headaches, mood swings, fatigue, cough, sinus congestion, agitation and more.

As gut pathogens, diseases, and dysbiosis go undetected or ignored, sometimes for years or even decades, the intestines become damaged and the mucosal lining is not able to do its job. For some patients, the diagnosis of an autoimmune disease is the first sign that there’s even something wrong with the gut.

This is why gut health is a primary area of focus in reversing autoimmune disease. But beyond autoimmunity, your gut also supports your thyroid health in other ways.

Your Gut and Thyroid Hormone Conversion

Remember, your thyroid produces mostly T4, which is inactive. It requires other tissues, like your gut to convert it to its active hormone T3, which is responsible for your energy, metabolism, body heat and much more.

About 20% of thyroid hormone conversion takes place in the gut and it is the job of your healthy gut flora to make sure you get the amount of T3 you need.

If your gut is not functioning optimally you can experience symptoms of hypothyroidism, even if you thyroid is healthy.


Gut Inflammation Inhibits Active Thyroid Hormone

Your microbiome regulates inflammation by inhibiting pro-inflammatory cytokines, like IL-6, TNF-alpha, NFK-b, and promoted anti-inflammatory cytokines like IL-10. If you’re not familiar with these terms, don’t worry. All you need to know is that the more these things proliferate, unregulated in your system, the more inflammation in the body.

When inflammation goes up, cortisol follows and this down-regulates the conversion to T3.

Constipation Reduces Thyroid Hormone

Constipation can create hormone imbalances that lead to increased levels of estrogen. As estrogen levels increase, so do proteins aimed at keeping the hormone bound. The same mechanisms that lead to excess estrogen being bound can cause thyroid hormone to also become unavailable.

Low levels of circulating thyroid hormone can cause impaired gut motility and constipation, which can perpetuate the cycle of hormone imbalance.

This is another example of how gut function is crucial to having adequate levels of thyroid hormone available.

Healing Your Gut

You must heal your gut if you are going to improve thyroid health, balance hormones and reverse your autoimmune condition.

As a natural medicine and lifestyle doctor, I work with women in developing a treatment protocol that is specific to their individual needs. It is also important to begin with lab testing to create a more targeted treatment plan, which can also ensure healing is not delayed. I recommend working with a licensed practitioner who understands the importance of conventional and functional lab testing and can interpret them in conjunction with your story.

Here are some of the recommendations I make to my patients wanting to heal their gut and improve their thyroid health. Again, it’s always best to do the work to understand what is at the root of your symptoms before you begin supplementing.

autoimmune thyroid disease and constipation

Four Phases to Gut Healing

1. Remove

All Potential Food Triggers. 

Remove any possible food irritants for 3-6 weeks. One of the best ways to do this is with an elimination diet. This involves removing the top food allergens and other possible aggravators from your diet for 3-4 weeks. These are: Gluten, Dairy, Corn, Soy, Nuts, Beans/Legumes (including peanuts), and stimulants like chocolate, black tea, and coffee.

Don’t hate me for saying coffee. I know no one likes to let that one go, but coffee may cross-react with gluten, irritating your intestines and well, you just don’t know if it is making your symptoms worse until it has been removed.

Unnecessary Medications. 

Remove NSAIDs, proton pump inhibitors (PPIs), unnecessary antibiotics, and birth control. Talk with your doctor before discontinuing meds.

Life Stressors. 

Like we mentioned above, chronic stress can actually change the makeup of your microbiome. It also disrupts the HPA-axis (hypothalamic-pituitary-adrenal), which affects pretty much all the hormones in your body.

Bacteria, Yeast, Parasites. 

Ask your doctor to test for and treat any potential bacterial or yeast overgrowth and to assess for any parasites or pathogens. Again, some of these critters can live on happily undetected. If you’re having any chronic gut or thyroid issues, best to test.

2. Replace

Digestive Enzymes. 

Important digestive enzymes can become depleted with age or underuse. Taking targeted digestive enzymes for a period of time can be helpful when we’re healing.

Betaine HCl. 

If you have hypochlorhydria (low stomach acid) or become very full with meals, you may need the help of some Betaine HCl. Ask your doctor about adding this to your regimen.

Consider a Combination Digestive Aid.

I typically recommend a combination product called Digest that is contains digestive enzymes, HCL, and ox bile for the most comprehensive support.

Digest is comprised of a blend of digestive enzymes along with betaine HCL to support optimal digestion of proteins, fats, and carbohydrates. If you've ever been “glutened” and suffered the effects, know this product contains the special protease DPP IV that breaks down gluten and lactase to digest dairy. The use of Digest before meals may be helpful when patients experience gas and bloating after eating, constipation, or a feeling of fullness after eating only a small quantity of food.

Digest is part of my Gut Repair Kit.

Download your FREE Hormone Starter Kit with Recipes to Heal Your Gut   and learn more about how optimizing thyroid health

3. Re-inoculate

Fermented Vegetables.

This is a great way to begin getting some beneficial bacteria going in your gut! Raw, cultured, organic vegetables like pickles, sauerkraut, and other fermented vegetables like beets and carrots can promote the growth of good bacteria in the gut.


I recommend women with a thyroid condition consider spore based probiotics, lactobacillus and bifido species, along with a other beneficial organisms. I typically start my patients with Women's Probiotic as I've seen this provide great results. Saccromyces boulardi is one strain that has been shown to protect against pathogens, increase beneficial immune response, protect gastrointestinal barrier function, and promote enzymatic activity so you can better absorb nutrients from your food!

Note: If your digestive symptoms get worse or you experience extreme gas or bloating when probiotic foods or supplements are introduced, I recommend reducing or eliminating probiotics and talking with your doctor about SIBO testing or fructose intolerance.

4. Repair

Curcumin Extract.

While eating and drinking turmeric is beneficial to your overall health, I recommend supplementation with the active constituent, curcumin, while healing the gut.


Glutamine feeds the cells of your intestine, helping create a healthy intestinal lining.

Ginger Root. 

Ginger root contains a number of constituents that help to reduce irritation and inflammation.

Zinc Carnosine.

A combination of the mineral zinc and the amino acid carnosine, this supplement increases healing time and boosts immune function.

Marshmallow Root.

Marshmallow root soothes and healing the intestinal lining and is good for the acute treatment of both constipation and diarrhea.

Aloe Vera.

Aloe is a potent anti-inflammatory that has been used with success in patients with Irritable Bowel Disease.

Getting to the root of your gut issues is an important step to healing your thyroid and your health. In my practice, I understand the importance of conventional and functional lab testing and can interpret them in conjunction with your story. I can help guide you on your next steps and help you understand your thyroid a whole lot better in my Thyroid Master Class.

If you want to dig deeper to explore your root cause and find out more about how to heal your thyroid, please consider attending my Thyroid Master Class.

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About The Author

Dr. Jolene Brighten

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Dr. Jolene Brighten, NMD, is a women’s hormone expert and prominent leader in women’s medicine. As a licensed naturopathic physician who is board certified in naturopathic endocrinology, she takes an integrative approach in her clinical practice. A fierce patient advocate and completely dedicated to uncovering the root cause of hormonal imbalances, Dr. Brighten empowers women worldwide to take control of their health and their hormones. She is the best selling author of Beyond the Pill and Healing Your Body Naturally After Childbirth. Dr. Brighten is an international speaker, clinical educator, medical advisor within the tech community, and considered a leading authority on women’s health. She is a member of the MindBodyGreen Collective and a faculty member for the American Academy of Anti Aging Medicine. Her work has been featured in the New York Post, Forbes, Cosmopolitan, Huffington Post, Bustle, The Guardian, Sports Illustrated, Elle, and ABC News. Read more about me here.