Fishy-smelling poop usually comes from something you ate, but it can also signal a gut infection, bacterial imbalance, or a rare metabolic condition. The smell itself comes from specific chemical compounds produced when bacteria in your intestines break down certain nutrients, particularly ones found in eggs, fish, organ meats, and legumes.
How Gut Bacteria Create a Fishy Smell
Your colon is home to trillions of bacteria that help digest food. When these bacteria break down foods rich in certain nutrients (choline, lecithin, and carnitine), they produce a compound called trimethylamine, or TMA. TMA has a distinctly fishy odor. Normally, your liver converts TMA into an odorless form before it causes problems. But when you eat large amounts of TMA-producing foods, or when something disrupts that conversion process, the fishy smell can show up in your stool.
Hydrogen sulfide is another major odor-producing compound in stool and gas. While it typically smells more like rotten eggs than fish, shifts in your gut bacteria can change the balance of these compounds and produce unfamiliar smells. When bacterial populations in the gut are thrown off, whether from antibiotics, illness, or dietary changes, the chemical profile of your stool changes with them.
Foods and Supplements That Cause It
Diet is the most common and least worrying explanation. Foods that are very high in choline are the main culprits, because choline is a direct precursor to that fishy-smelling TMA compound. The biggest sources include whole eggs, organ meats (especially liver), cruciferous vegetables like broccoli and cabbage, legumes and soy products, salmon, cod, shrimp, and ground beef. Even fast foods like cheeseburgers, chicken nuggets, and lasagna contain significant amounts.
Fish oil and omega-3 supplements are another frequent cause. If you recently started taking fish oil capsules and noticed a change in stool odor, that’s likely the connection. Lecithin supplements, sometimes taken for brain health, are also a direct source of the compounds your gut bacteria convert into TMA. Reducing your intake of these foods or supplements for a few days is the simplest way to test whether diet is responsible.
Gut Infections and Parasites
Giardia, a common waterborne parasite, produces characteristically smelly, greasy stools that can float. Other symptoms include diarrhea, gas, stomach cramps, and nausea. You can pick up giardia from contaminated water sources, including streams, lakes, and occasionally public pools. If your fishy-smelling stool came on suddenly and is accompanied by diarrhea or cramping, an infection is worth considering.
Bacterial overgrowth in the small intestine (sometimes called SIBO) can also shift stool odor. When bacteria that normally live in the colon migrate into the small intestine and multiply, they ferment food earlier in the digestive process, producing excess gas and unusual-smelling stool. Bloating, cramping, and changes in bowel habits often accompany it.
Trimethylaminuria: The “Fish Odor” Condition
There is a rare genetic condition called trimethylaminuria in which the liver enzyme responsible for neutralizing TMA doesn’t work properly. People with this condition accumulate TMA in their body, and it escapes through sweat, breath, urine, and stool, all carrying a fishy odor. The global prevalence is estimated at roughly 1 in 200,000 to 1 in 1,000,000 people, so it’s uncommon.
If the fishy smell has been persistent your entire life or runs in your family, trimethylaminuria is worth investigating. Diagnosis involves a urine test, sometimes after eating a diet loaded with eggs, cabbage, fish, and shellfish for three days to provoke TMA production. The test measures the ratio of TMA to its odorless form in urine. In healthy people, more than 80% of TMA gets converted to the odorless version. In people with trimethylaminuria, that conversion is significantly impaired.
There’s no cure, but the condition is manageable. People with trimethylaminuria typically reduce their intake of high-choline foods, and some benefit from riboflavin (vitamin B2) supplements, which can help support whatever residual enzyme activity remains. The condition isn’t dangerous, but the social and psychological impact can be significant.
A Note for Women: It May Not Be Your Stool
Because of the proximity of the vaginal and rectal areas, a fishy smell you notice when using the bathroom may not actually be coming from your stool. Bacterial vaginosis (BV) is a very common vaginal infection whose hallmark symptom is a “fishy” smelling discharge, typically off-white or gray. If you’re noticing the smell primarily when wiping or on underwear rather than in the toilet bowl itself, BV is a more likely explanation than a digestive issue.
Dietary Changes That Help
If you suspect diet is the cause, reducing high-choline foods is the most direct approach. That means cutting back on eggs (especially yolks), liver, soy products, and cruciferous vegetables like broccoli, Brussels sprouts, and cauliflower. You don’t need to eliminate these permanently. Try reducing them for a week or two and see if the smell changes.
If you’re taking fish oil, lecithin, or carnitine supplements, pause them temporarily and note any difference. For people with confirmed trimethylaminuria, a long-term low-choline diet is the primary management strategy, though it requires careful planning since choline is an essential nutrient your brain and liver need.
Signs That Need Medical Attention
A temporary change in stool odor after a big seafood dinner is nothing to worry about. But certain accompanying symptoms point to something that needs evaluation: blood in your stool, black or unusually pale stools, unexplained weight loss, persistent fever or chills, or ongoing abdominal pain. If the fishy smell has persisted for weeks without a clear dietary explanation, or if it’s paired with chronic diarrhea, a stool test can check for infections like giardia, and a urine test can screen for trimethylaminuria.