Can Hypothyroidism Cause Diarrhea?

Hypothyroidism is classically associated with constipation, not diarrhea. Slowed gut motility is one of the most consistent gastrointestinal effects of low thyroid hormone levels, and large studies confirm that constipation is the far more typical bowel complaint. Yet people with hypothyroidism do sometimes develop diarrhea, and the reasons are more varied and less intuitive than you might expect. The pathways range from bacterial overgrowth triggered by sluggish intestines to autoimmune conditions that travel alongside thyroid disease to, paradoxically, the very constipation that defines the condition.

Why Constipation Is the Expected Symptom

Thyroid hormones have a direct effect on the muscles lining the digestive tract. When those hormone levels drop, the rhythmic contractions that push food through your intestines slow down. A study measuring gastrointestinal transit in thyroid disease found that when patients who were hyperthyroid became hypothyroid after treatment, their gut transit time roughly tripled, and when hypothyroid patients received thyroid replacement, transit time sped back up significantly.¹ That slowing is the primary reason constipation is so strongly linked to an underactive thyroid.

The mechanism goes beyond simple muscle sluggishness. Animal research shows that hypothyroidism suppresses the activity of sodium-potassium pumps in the colon wall, which are involved in fluid and electrolyte absorption.² And hypothyroid animals show reduced nutrient transport across the intestinal lining compared to animals with normal thyroid function.³ So the gut in hypothyroidism is not just slow; its basic absorptive and transport machinery is running at a lower gear. A review of thyroid-related gastrointestinal problems summed it up plainly: hyperthyroidism commonly produces diarrhea and malabsorption, while hypothyroidism frequently produces constipation.⁴

All of that makes diarrhea seem like the last thing you would expect. But the body does not always follow the textbook, and several conditions closely tied to hypothyroidism can flip the picture.

When Slow Guts Invite Bacterial Overgrowth

One of the more common reasons a person with hypothyroidism develops diarrhea is small intestinal bacterial overgrowth, often shortened to SIBO. Normally, the small intestine hosts a relatively modest population of bacteria compared to the large intestine. Regular muscular contractions sweep bacteria downstream, keeping the small intestine from getting overcrowded. When hypothyroidism slows those contractions, bacteria that would otherwise be swept along can accumulate in the small intestine. Those excess bacteria ferment food prematurely, producing gas, bloating, cramping, and frequently diarrhea.

Research has established that reduced motility is a clear risk factor for SIBO and that SIBO is common in patients with hypothyroidism.⁵ The authors of that work recommended that patients with hypothyroidism who have persistent gastrointestinal symptoms, especially if those symptoms do not match the expected constipation pattern, should be evaluated for SIBO. SIBO is treatable, usually with a course of antibiotics, but it tends to recur if the underlying slow motility is not addressed with adequate thyroid hormone replacement.

This is one of the more frustrating scenarios: you have hypothyroidism, your gut is sluggish, and instead of the constipation your doctor anticipated, you end up with diarrhea because that sluggishness created a secondary problem. It can be confusing for both patients and clinicians if SIBO is not on the radar.

Autoimmune Conditions That Tag Along

The most common cause of hypothyroidism in developed countries is Hashimoto’s thyroiditis, an autoimmune condition in which the immune system gradually destroys the thyroid gland. People with one autoimmune disease are statistically more likely to develop another, and several of the autoimmune conditions that cluster with Hashimoto’s directly cause diarrhea.

Celiac Disease

Celiac disease is an autoimmune reaction to gluten that damages the lining of the small intestine, causing diarrhea, malabsorption, and weight loss. It shows up at elevated rates in people with autoimmune thyroid disease, and the reverse is also true: autoimmune thyroiditis is more prevalent in patients who have celiac disease.⁶ A review of endocrine complications in celiac disease noted that in adults, autoimmune thyroid disease, especially hypothyroidism, commonly co-exists with celiac disease.⁷

One thing that makes this tricky: celiac disease does not always look the way you would expect. A study of patients with autoimmune thyroiditis found that about 9% tested positive for celiac antibodies, but most of those patients were actually overweight, and only one reported diarrhea as a symptom.⁸ Celiac disease can quietly cause intestinal damage with minimal obvious symptoms for years. So if you have hypothyroidism and develop unexplained diarrhea, even mild or intermittent diarrhea, celiac disease is worth screening for.

There is also a practical wrinkle. The intestinal damage from celiac disease can impair your body’s ability to absorb levothyroxine, the standard thyroid replacement medication. That means untreated celiac disease could make your hypothyroidism harder to control, creating a feedback loop where both conditions worsen each other.

Microscopic Colitis

A less well-known companion is microscopic colitis, a condition where chronic inflammation in the colon causes persistent watery diarrhea, even though the colon looks normal under standard colonoscopy. It can only be diagnosed with tissue biopsies viewed under a microscope. A large nationwide study in Sweden found that autoimmune thyroid diseases were significantly more common in patients with microscopic colitis than in the general population, with roughly 12% of microscopic colitis patients having an autoimmune thyroid disease compared to about 8% in matched controls.⁹ The association was strongest in patients diagnosed with microscopic colitis before age 50.

Microscopic colitis is an underdiagnosed condition in general. If you have autoimmune hypothyroidism and chronic watery diarrhea with no clear cause, it is worth specifically requesting the biopsies that diagnose it, since a standard colonoscopy will miss it every time.

Inflammatory Bowel Disease

The relationship between hypothyroidism and inflammatory bowel disease (IBD) is more complex and less straightforward than the celiac or microscopic colitis connections. A genetic analysis using Mendelian randomization actually found that genetically predicted hypothyroidism was associated with a reduced risk of Crohn’s disease, not an increased risk.¹⁰ That does not mean a person cannot have both conditions, but the data do not suggest that hypothyroidism drives IBD the way it clusters with celiac disease. If you have hypothyroidism and severe or bloody diarrhea, IBD should be on the differential, but it is not a likely autoimmune co-traveler in the way celiac disease is.

Overflow Diarrhea From Severe Constipation

This one surprises a lot of people. Severe, long-standing constipation can itself cause diarrhea. When a large mass of hard stool becomes impacted in the rectum or lower colon, liquid stool from higher up can leak around the obstruction and come out as watery diarrhea. Clinicians call this overflow diarrhea or paradoxical diarrhea, and it can look and feel indistinguishable from an infectious or inflammatory cause.¹¹

Since hypothyroidism is a well-established cause of chronic constipation, and undertreated hypothyroidism can leave the bowels profoundly sluggish, fecal impaction is a real risk, particularly in older adults or people whose thyroid medication is not optimally dosed. The danger here is misdiagnosis: a patient comes in reporting diarrhea, gets treated with anti-diarrheal medication, and the underlying impaction worsens. If you have hypothyroidism and develop sudden watery diarrhea after a period of increasingly severe constipation, overflow diarrhea should be considered before reaching for anti-diarrheal drugs.

Medication-Related Diarrhea

Levothyroxine, the synthetic thyroid hormone used to treat hypothyroidism, is one of the most commonly prescribed medications in the world. When dosed correctly, it should not cause diarrhea. But several medication-related scenarios can lead to loose stools in people being treated for hypothyroidism.

Too Much Levothyroxine

If the dose is too high, you are effectively creating a state of excess thyroid hormone, and diarrhea is a recognized symptom of that excess. A systematic review of levothyroxine overdose cases found diarrhea in about 10% of reported cases.¹² This does not have to involve dramatic overdoses; even moderately excessive dosing, or a dose that was once appropriate but became too much after a change in body weight, kidney function, or other medications, can tip you into mild hyperthyroid territory and bring on diarrhea along with symptoms like anxiety, heart palpitations, and heat intolerance.

Supplement and Drug Interactions

On the flip side, certain common supplements can reduce how much levothyroxine your body absorbs. Calcium and iron are the classic offenders, but magnesium supplements also interfere. A crossover trial in healthy subjects found that taking magnesium aspartate alongside levothyroxine reduced thyroxine absorption by about 12%.¹³ If poor absorption leaves you undertreated, your doctor may increase the dose. Then if you stop the supplement or change when you take it, you could suddenly be absorbing more levothyroxine than intended, creating the excess-hormone scenario described above.

Lactose Intolerance and Tablet Formulation

Some levothyroxine tablets contain lactose as a filler. If you have lactose intolerance, the lactose in the tablet can contribute to bloating, gas, and diarrhea, while simultaneously reducing absorption of the medication itself. A case report described a woman whose severe hypothyroidism persisted despite escalating doses of levothyroxine tablets; the cause turned out to be lactose intolerance impairing absorption of the tablet formulation. Switching to a lactose-free powder form of levothyroxine at the same dose normalized her thyroid levels.¹⁴ If you are lactose intolerant and taking levothyroxine tablets, it is worth asking your doctor about a lactose-free formulation, both for GI comfort and for more reliable absorption.

How to Tell What Is Causing Diarrhea in Hypothyroidism

Because the possible causes are so varied, figuring out why someone with hypothyroidism has diarrhea requires some detective work. A few practical considerations can help narrow the field:

• Check thyroid levels first: If your TSH is suppressed below the normal range, your levothyroxine dose may be too high, and the diarrhea may simply be a sign of overtreatment.
• Ask about constipation history: If you were significantly constipated before the diarrhea started, especially if you have not had a bowel movement in days, overflow diarrhea from impaction should be considered.
• Screen for celiac disease: Simple blood tests for tissue transglutaminase (tTG) and endomysial antibodies (EMA) can flag celiac disease. Given how commonly it co-occurs with autoimmune thyroid disease, screening is reasonable even without classic celiac symptoms.
• Consider SIBO testing: A hydrogen breath test can help identify bacterial overgrowth. If your diarrhea is accompanied by significant bloating and gas, particularly after meals, SIBO is a strong candidate.
• Request biopsies during colonoscopy: If you are having a colonoscopy for chronic diarrhea and it looks visually normal, biopsies from the right colon should be taken specifically to check for microscopic colitis.
• Review your supplement routine: Calcium, iron, and magnesium taken near your levothyroxine dose can impair absorption. Taking these supplements at least four hours apart from your thyroid medication is standard advice.

None of these steps are exotic or hard to access, but they do require awareness that diarrhea in a hypothyroid patient is not just some random unrelated symptom. Each of these causes connects back to the thyroid condition in some way, whether through slowed motility, autoimmune overlap, or medication interactions.

Hypothyroidism and the Gut in Newborns

The gut-thyroid connection shows up from the very beginning of life. Infants born with congenital hypothyroidism, where the thyroid gland is absent or severely underdeveloped, present with a distinctive set of gastrointestinal signs. These include a delay in the onset of stooling, abdominal distension, and vomiting.¹⁵ The pattern here is the same as in adults: profound hypothyroidism slows the gut, and the immediate consequence is sluggish bowel function, not diarrhea. Diarrhea in a newborn with hypothyroidism would prompt clinicians to look for a separate cause rather than attributing it to the thyroid deficiency itself.

Newborn screening programs in most countries now catch congenital hypothyroidism within days of birth through a routine heel-prick blood test, so severe cases are usually treated with thyroid hormone replacement before major gut complications develop. But the newborn presentation reinforces the broader point: when thyroid hormones are absent or severely deficient, the gut’s first response is to slow down, and any diarrhea that develops alongside hypothyroidism calls for a separate explanation.

Why the “Constipation Only” Story Is Too Simple

Textbooks and patient information sheets almost always list constipation under hypothyroidism and diarrhea under hyperthyroidism, as though the two conditions produce neatly opposite GI symptoms. That framework is not wrong, but it creates a blind spot. When a patient with confirmed hypothyroidism reports diarrhea, the instinct can be to dismiss it as unrelated or to assume it must be something else entirely. In reality, the thyroid condition is often the root cause, just through a less direct route than simple hormone-mediated gut slowing.

Bacterial overgrowth from slow motility, autoimmune co-travelers like celiac disease and microscopic colitis, overflow diarrhea from fecal impaction, and medication dosing issues all connect back to the hypothyroid state or its treatment. The diarrhea is not random. It is a downstream consequence of a body dealing with low thyroid hormones and the cascade that follows. Recognizing that connection is what turns a confusing symptom into a solvable problem.