The Thyroid-Gut Connection

How gut health affects the thyroid

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 all you can do. Period. 

I’d even guess there was no mention of your gut health, let alone the thyroid-gut connection. In the conventional medical 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 your thyroid function. And since thyroid and gut health conditions are often overlooked or misdiagnosed, it’s essential to understand the thyroid-gut connection so you can advocate for yourself effectively.

Can Thyroid Cause Gut Problems?

Thyroid hormones are crucial in our ability to conceive, sleep patterns, mental health, energy levels, and how well we digest, assimilate, and absorb our food and nutrients. Thyroid hormones like thyroxine (T4) and triiodothyronine (T3) define basal metabolism (the amount of energy expended to complete a biological task/function).

But I don’t have digestive issues like constipation, diarrhea, or bloating.

Yes, but it is still possible to have food sensitivities, dysbiosis, and other gut conditions – even Celiac disease! – without any overt gut symptoms at all. Estimates indicate that most people newly diagnosed with Celiac disease do not present with gastrointestinal symptoms. 

It’s well-documented that thyroid and digestive issues often coexist.

Gastrointestinal symptoms of thyroid dysfunction are numerous and include trouble swallowing, heartburn, indigestion, reduced acid production, nausea or vomiting, gallbladder complaints, abdominal discomfort, gas, bloating, diarrhea, constipation, and general digestive complaints, including Irritable Bowel Syndrome (IBS).

Poor gut health can make the thyroid function worse, and the thyroid can affect gut health. It is a two-way street. Let’s dive into why.

The thyroid-gut-autoimmunity connection

The gut microbiome contains about 70% of the immune system and is an important influence on thyroid function, specifically on autoimmune thyroid diseases like Hashimoto’s thyroiditis and Graves. This influence can be explained (at least in part) by compromised intestinal barrier function (aka intestinal hyperpermeability or “leaky gut”), which allows antigens to pass more quickly and trigger autoimmune disease in genetically susceptible individuals. When a leaky gut occurs, it affects our body’s ability to assimilate and absorb critical micronutrients such as iodine, selenium, zinc, iron, B vitamins, vitamin A, and tyrosine which are essential to healthy thyroid function. These micronutrients are often deficient in those with autoimmune thyroid disease.

Although not fully understood, gut microbiota also influences the conversion of T4 to T3—T3 being the active form of thyroid hormone. Iodothyronine deiodinase enzymes play a central role in converting T4 to its active form, T3. 

Hashimoto’s and Graves often coexist with specific digestive diseases, including Celiac Disease and Non-celiac wheat sensitivity (NCWS).

People with autoimmune thyroid disease are 4 to 5 times as likely to develop Celiac Disease as the general population.

Gut Health Tests To Ask Your Doctor About

Good thyroid health starts in the gut. Simple, gut-directed therapies can help you to resolve frustrating symptoms, reduce thyroid inflammation, reduce thyroid antibodies, and, in some cases, reduce thyroid medication.

  • A full thyroid panel includes TSH, free T4, free T3, reverse T3, and Thyroglobulin (TG) and Thyroid Peroxidase (TPO) antibodies. To learn more about why I run all these tests, and not just TSH, check out: A Functional Medicine Doctor’s Approach to Hashimoto’s Thyroiditis and Hypothyroidism.
  • Complete Blood Count (CBC) and Iron Panel to check for anemia and iron levels
  • Nutrient testing for zinc, selenium, Vitamin D, Vitamin A, and some of the B vitamins (homocysteine can also be a helpful marker for B vitamins).
  • You may need to rule out H/Pylori or SIBO if you have a lot of bloating.

4 Steps To Improve Gut and Thyroid Health

  1. Remove Processed Foods with an anti-inflammatory diet

You should start with an anti-inflammatory diet rich in nutrient-dense foods, including foods high in selenium, zinc, iron, B vitamins, and vitamin A, and foods rich in healthy fats like olive oil, nuts, avocados, and omega-3s.

Some patients have also to eliminate trigger foods that cause unwanted symptoms. You can do this with an elimination diet or food sensitivity testing. I recommend patients eliminate gluten and dairy if they experience bloating, constipation, or abdominal pain, as these are consistently seen in the literature to cause symptoms. 

2. Eliminate Toxins

I always counsel my patients on adopting a low-tox lifestyle, which means drinking clean filtered water, breathing clean air, and cleaning up their beauty regimens. For more information, listen to my podcast episode with Megan Mikkelson of Detox by Design.

3. Get on the Right Medication

I advocate using safe, properly-dosed medications. A few of the medicines I commonly prescribe include desiccated thyroid hormones like Armour, NP Thyroid, or the standard Synthroid. But, as always, this is an individualized discussion with your provider based on risks and benefits.

As your gut becomes healthier and your symptoms resolve, you may start to absorb thyroid medication better. Lab tests and fine-tuning with your health provider can help to optimize your medication dose. Most patients do not need alternative thyroid medication, such as combined T4/T3 therapy.

Your thyroid also plays a super important role in the production of stomach acid which can result in symptoms like GERD, nutrient deficiencies, and other digestive ailments like SIBO (small intestinal bacterial overgrowth) and SIFO (small intestinal fungal overgrowth).

Research has also shown that hypothyroidism causes gastrointestinal dysfunction by significantly reducing gastroesophageal motility. This is why many people with low thyroid function benefit from supplementation with Betaine HCl. Betaine HCL allows the protein to be broken down, which aids digestion but also reduces inflammation which can reduce pain. 

4. Smart Supplements

For many patients, I also recommend multi-strain probiotics. They include research-validated probiotic strains from all three major probiotic categories:

  • Lactobacillus & bifidobacterium species
  • Saccharomyces Boulardii (a probiotic fungus)
  • Bacillus species (soil-based probiotics)


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

Digestive enzymes and HCL can also be useful. For more information, check out this post.


Since so many people with gut/thyroid issues have nutrient deficiencies, I typically recommend supplementing with high-quality multivitamins with vitamin A, methylated B vitamins, iron, selenium, vitamin D, and zinc, in addition to dietary changes.

Curcumin Extract.

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

Ginger Root. 

Ginger root contains several constituents that help to reduce irritation and inflammation.

Marshmallow Root.

Marshmallow root soothes and heals the intestinal lining and is good for treating constipation and diarrhea.

Aloe Vera.

Aloe is a potent anti-inflammatory used successfully in patients with Irritable Bowel Disease.

Getting to the root of your gut issues is important 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. In my practice, personalize these recommendations based on testing and your unique needs and vulnerabilities.

Ready to do something about your chronic digestive issues and thyroid health?

I’m accepting a limited number of new patients for integrative medicine consults. Click here to learn more about becoming a patient, and I look forward to hearing from you!

20210321 123559

Hey, it's Dr. Jen.

I am so glad you are here! OB/GYN. Mamma of 4. Self-proclaimed foodie. Avid outdoor enthusiast. I am a hormone guru who healed my PCOS and hypothyroidism through diet and lifestyle shifts.

I help women identify and address the root causes of their hormone and digestive symptoms.

Get Help With Your Hormones...

Your Personalized Holistic Health Plan

Virtual Visits

Get personalized holistic health care and support online.

Dr. Jennifer Roelands

I’m an Integrative Medicine trained OB/GYN and expert in PCOS who healed my own PCOS and hypothyroidism.

I partner with patients to uncover the underlying causes of their unexplained symptoms so they can feel like themselves again.

Using holistic medicine, functional testing, and mind-body tools I create personalized plans unique to your root cause(s) to remove obstacles to healing, correct imbalances, and allow the body to heal.

I’ve helped hundreds of patients transform their health and I welcome you to find out how this comprehensive approach to deep healing can do the same for you.

Request an Appointment


301 W. Bastanchury, Suite 140
Fullerton, CA 92835


Monday-Friday: 8AM - 5PM


Request an Appointment

Which service are you interested in?(Required)

Scroll to Top