Quick answer: Thyroid hormones help set the pace of the whole digestive tract, so an underactive thyroid (hypothyroidism) is commonly associated with slower transit, constipation and bloating. Studies have also linked hypothyroidism with a higher rate of small intestinal bacterial overgrowth (SIBO), possibly because slower movement makes it harder to clear bacteria from the small intestine. The relationship works the other way too: coeliac disease, low stomach acid, some medications and even coffee can reduce how well levothyroxine is absorbed. If you have gut symptoms and a thyroid condition, it is worth asking your doctor to check your thyroid levels before looking elsewhere, and to review how you take your medication.
Many people who come to me with constipation, bloating or a sluggish gut also mention an underactive thyroid, or a family history of one. Sometimes the connection has never been explained to them. The thyroid and the gut are closely linked, and supporting one often means paying attention to the other. If constipation is your main concern, you may also find the root causes of chronic constipation useful.
Can an underactive thyroid cause constipation and bloating?
Yes. Thyroid hormones influence the muscles and nerves that move food through the gut. When levels are low, transit can slow down from the oesophagus to the colon, which is commonly associated with constipation, bloating and feeling full quickly. Reviews of the thyroid and the gut describe these changes across the whole digestive tract. Constipation can also be one of several signs, alongside tiredness, feeling cold, dry skin and hair changes, that thyroid levels need checking.
Is hypothyroidism linked to SIBO?
Several studies suggest so. In one study, people with a history of hypothyroidism had a higher rate of SIBO on breath testing than controls. A larger cohort study found that levothyroxine use and impaired clearance of the gut were among the strongest factors associated with SIBO. Slower movement in the small intestine is the most likely link. This does not mean everyone with hypothyroidism has SIBO, but it is worth considering if bloating and changes in bowel habit persist even with well-managed thyroid levels. Read more about SIBO root causes and symptoms.
Does gut health affect levothyroxine absorption?
It can. Levothyroxine is absorbed mainly in the small intestine and needs an acidic stomach to dissolve well. A review of factors affecting its absorption lists coeliac disease, low stomach acid (including from acid-suppressing medicines), H. pylori infection, and taking it with coffee, food, calcium or iron supplements. If your dose keeps needing to go up, or your levels are hard to stabilise, it is worth discussing these factors with your doctor. Low iron can also travel with thyroid and gut issues; see low ferritin and the gut.
When to see your doctor first
- Blood in or on the stool, or black stools
- Unintentional weight loss, or a new, persistent change in bowel habit
- Severe constipation with vomiting, a swollen abdomen or inability to pass wind
- Difficulty swallowing or a lump in the neck
- Marked tiredness, low mood, feeling very cold or a slow heart rate
- Palpitations, tremor or weight loss if your dose was recently changed
What about Hashimoto's and the microbiome?
Hashimoto's thyroiditis, the most common cause of hypothyroidism in many countries, is an autoimmune condition. Research on the gut–thyroid axis suggests that the microbiome, gut barrier and absorption of nutrients such as selenium, iron and vitamin D may all play a role. These links are still being studied, and there is no gut-based approach that replaces thyroid medication. It is reasonable, though, to look after the gut as part of a wider plan.
What can support your gut if you have hypothyroidism?
- Ask your doctor to check your thyroid levels if gut symptoms change or worsen.
- Take levothyroxine as advised, usually on an empty stomach with water, and keep coffee, food, calcium and iron supplements apart from it.
- Support transit with gradual fibre, enough fluid, regular meals and daily movement.
- Include selenium- and iodine-containing foods as part of a varied diet (for example fish, eggs and a few Brazil nuts), without high-dose supplements unless advised.
- Ask about coeliac screening if you have ongoing gut symptoms, as coeliac disease is more common with autoimmune thyroid disease.
Any supplement is optional, should be individualised and checked with your doctor, because some can interfere with thyroid medication or tests (biotin, for example, can affect blood results).
Thyroid managed, but your gut still sluggish?
Let's look at your digestion, absorption and daily habits together, alongside your doctor's care, and find what may help your gut feel more settled. A free call, with no commitment.
Book your free 15-minute call →Frequently asked questions
Can thyroid problems cause IBS?
An underactive or overactive thyroid can cause gut symptoms that look like IBS. That is why thyroid tests are often part of the work-up for new bowel symptoms.
Should I take levothyroxine with coffee?
Coffee can reduce levothyroxine absorption. Many people are advised to wait 30 to 60 minutes after taking it before coffee or breakfast. Follow your doctor's or pharmacist's advice.
Does an overactive thyroid affect the gut?
Yes. Hyperthyroidism tends to speed up transit and is commonly associated with more frequent or loose stools.
Does going gluten-free help Hashimoto's?
There is no strong evidence that everyone with Hashimoto's benefits from a gluten-free diet. If you have gut symptoms, ask your doctor about coeliac testing before removing gluten.
References
- Ebert EC. The thyroid and the gut. J Clin Gastroenterol. 2010. PubMed: PMID 20351569
- Lauritano EC, Bilotta AL, Gabrielli M, et al. Association between hypothyroidism and small intestinal bacterial overgrowth. J Clin Endocrinol Metab. 2007. PubMed: PMID 17698907
- Brechmann T, Sperlbaum A, Schmiegel W. Levothyroxine therapy and impaired clearance are the strongest contributors to small intestinal bacterial overgrowth: results of a retrospective cohort study. World J Gastroenterol. 2017. PubMed: PMID 28223728
- Skelin M, Lucijanić T, Amidžić Klarić D, et al. Factors Affecting Gastrointestinal Absorption of Levothyroxine: A Review. Clin Ther. 2017. PubMed: PMID 28153426
- Virili C, Stramazzo I, Centanni M. Gut microbiome and thyroid autoimmunity. Best Pract Res Clin Endocrinol Metab. 2021. PubMed: PMID 33648848
This article is for educational purposes and is not medical advice. Nutritional therapy does not replace medical care. Always work with your doctor for any persistent or new symptoms and before making changes to your care, medication or supplements.