Join Our Thyroid Awareness Campaign this January!

January is Thyroid Awareness Month

Join us this January to spotlight thyroid health. Participate, share, and spread awareness for a chance to win exciting prizes!

What Is The Thyroid-Gut Axis?

This is an overview of the thyroid-gut axis. Learn how to restore proper gut function for better thyroid health.
What Is The Thyroid-Gut Axis?
Last updated:
Medically Reviewed by:

In this article:

Hippocrates, the infamous Greek physician, stated, "All disease begins in the gut." For thousands of years now, speculation is that there is a connection between the gut and disease. Only recently, science is starting to uncover the truth behind the gut and is learning just how influential it is on our health. Ahead, a look at the complex relationship between your thyroid, gut health, and immune system.

Why does the gut matter?

Most of us take our digestive systems for granted. We know it serves to digest our food, which in turn gives us energy. Beyond that, few of us are well-acquainted with just how impressive this system is overall. 

Unlike other organ systems, the contents of the digestive tract can reside outside of the body. For example, food and other materials enter this hollow system regularly without causing infection. Suppose outside contents enter any other body system, such as your skin, muscles, or bones. In that case, it can lead to tissue infection and severe illness. Therefore, the gut must have an incredible defense system to keep harmful substances from absorbing through your gut tissues into your bloodstream.

Beyond filtering substances, your gut is home to trillions of diverse bacteria, creating your gut microbiome. Most of your gut bacteria live in the colon, but they are also in the small intestine. This symbiotic relationship between gut bacteria and humans is vital for our health. We need a healthy microbiome to digest dietary fibers properly and for vitamin synthesis. 

Some research on the gut-brain axis suggests that an unhealthy microbiome can lead to mental disorders like anxiety, depression, schizophrenia, and autism. 

The immune system and the gut

Did you know that your immune system mostly lives in your gut? Indeed, 70% of your immune system resides along your digestive tract. 

The portion of your immune system that lives in your gut is called the gut-associated lymphoid tissue (GALT). These lymph tissues store immune cells that defend our bodies by attacking foreign invaders and producing antibodies. Your gut bacteria and immune system often work together to perform these protective functions.

Problems arise when the GALT loses its ability to protect the body, and you have a bacterial imbalance. One of the key features of disruption in this system is leaky gut syndrome. Leaky gut is the syndrome in which your intestinal walls (or barriers) become permeable to larger proteins that may cause damage to other organs in your body. These proteins enter the bloodstream, causing your immune system to become hyperactive to the point where it attacks healthy tissues. 

When the immune system becomes overactive, it can lead to autoimmune diseases like Hashimoto's thyroiditis (HT). 

Understanding the thyroid-gut axis

A study published in the journal Thyroid found that patients with Hashimoto's have microbial dysbiosis. Thus, an imbalance in your gut microbiome may not only cause the disease but may worsen it. Bacterial imbalances can lead to inflammation in the gut, which in turn exacerbates intestinal permeability. Inflammation of targeted tissues, like the thyroid, is a hallmark sign of autoimmune disorders.

Limited offer

20% off your first Thyroid Test

Test your thyroid levels from home and know your levels in days
Use code GETBETTER at checkout
Use code
Oops! Something went wrong while submitting the form.

Thyroid hormone conversion

Gut bacteria not only keep your immune system in check, but they also play an essential role in converting inactive T4 into active T3. Estimates suggest that about 20% of T4 is converted to T3 in the digestive tract, while the liver converts the rest. Because of the digestive system's role in thyroid hormone conversion, people with poor gut function often have thyroid symptoms but normal thyroid lab results. Medical providers refer to this state as euthyroid sick syndrome


Stress also plays a role in T3 conversion in the gut. When cortisol levels are high, active T3 levels decrease. Stress is a protective response by the body that, over time, can lead to chronic inflammation, and you guessed it, autoimmune diseases. 

Poor thyroid function on the gut

Thus far, we have seen how gut dysbiosis can affect your thyroid and the hormones it produces. However, just like the gut affects the thyroid, the thyroid affects the gut, too. 

Thyroid hormones are influential in the tight junctions between cells in the small intestine. Tight junctions are pivotal in creating an impenetrable membrane serving as a barrier between the gut and the rest of the body—the thyroid hormones T3 and T4 help keep those junctions tight. Thyroid-stimulating hormone (TSH) also has effects on the GALT. 


12 Week Hashimoto's
Health Plan


Healing the thyroid-gut axis

There are so many different reasons why a person may have a disrupted gut-thyroid axis. Hence, the best place to start is with a thyroid doctor to get to the root cause of your thyroid dysfunction. Treating hypothyroidism usually starts with replacing low thyroid hormone levels with thyroid hormone replacement medication. Most people require medication like levothyroxine for the rest of their life.  

Treating thyroid dysfunction often goes beyond medication. People with thyroid disease often have digestive issues from several factors, including diet, stress, health conditions, and genetics.

To support better thyroid health, you have to heal the gut, too. Yet, as seen by the relationship between the two systems, you have to manage the two systems simultaneously. This process is complicated and often takes a multifaceted approach to healing—there is no one-size-fits-all.

There are many ways of eating that may support the thyroid-gut axis like a gluten-free diet, iodine-free diet, Specific Carbohydrate Diet, GAPS diet, Paleo diet, the autoimmune protocol (AIP), soy-free diet, dairy-free diet, low-FODMAP diet, or the Body Ecology Diet. It can feel overwhelming to know where to start. The common thread behind all these nutritional interventions is a focus on removing reactive foods, replacing them with healing foods, and replenishing nutrients.

Generally speaking, functional medicine has used the 4R protocol for years to support gut health:

  1. REMOVE dietary triggers like gluten, dairy, sugar, etc.⁠
  2. REPLACE with digestive supports like hydrochloric acid and digestive enzymes.⁠
  3. REINOCULATE with probiotics and fermented foods to displace the pathogenic bacteria with beneficial bacteria.⁠
  4. REPAIR anything you're deficient in with nutrient-dense foods and supplementation.⁠

More specifically, we recommend working in collaboration with your thyroid care team to first optimize your thyroid medication and then design a healing diet appropriate for your needs. 

Dealing with Hypothyroidism?  Video chat with a thyroid doctor

Get answers and treatments in minutes without leaving home - anytime. Consult with a U.S. board certified doctor who only treats hypothyroidism via high-quality video. Insurance accepted.


Share article:

Julia Walker, RN, BSN

Clinical Nurse

Julia Walker, RN, BSN, is a clinical nurse specializing in helping patients with thyroid disorders. She holds a Bachelor of Science in Nursing from Regis University in Denver and a Bachelor of Arts in the History of Medicine from the University of Colorado-Boulder. She believes managing chronic illnesses requires a balance of medical interventions and lifestyle adjustments. Her background includes caring for patients in women’s health, critical care, pediatrics, allergy, and immunology.

Read more

Is Paloma Right For Me?

Hypothyroidism is a long-term commitment and we’re committed to you. Schedule a free, no-obligation phone consultation with one of our intake specialists to find out more.

Schedule a call
thyroid hormone for hypothyroidism

Find out if Paloma is right for you. Schedule a free call with one of our health care advisors.

Schedule a Call