Why Does My Poop Smell Like Mothballs?

The mothball-like smell in your stool almost certainly comes from two chemicals called indole and skatole, which are natural byproducts of bacteria in your colon breaking down the amino acid tryptophan. A landmark gas chromatography study found that these compounds, long assumed to be responsible for the general stink of feces, actually produce a distinctly naphthalene-like “mothball” odor rather than the broader sulfurous smell most people associate with a bathroom.

That finding reframes the question: the mothball smell is not some exotic warning sign. It is actually one of the core components of normal stool odor, and what varies from person to person, and day to day, is how much of it your gut bacteria are producing relative to other volatile compounds.

What Skatole and Indole Actually Are

Tryptophan is an essential amino acid you get from food. Your body absorbs most of it in the small intestine, but whatever escapes digestion travels down into the colon. There, trillions of bacteria ferment it. One of the main products of that fermentation is indole. A closely related compound, skatole (also called 3-methylindole), forms through a slightly different bacterial pathway that routes tryptophan through an intermediate molecule called indole-3-acetate.

Both indole and skatole belong to a family of chemicals called benzopyrroles. In concentrated or crystalline form, they smell strikingly like naphthalene, the active ingredient in traditional mothballs. At very low concentrations, indole actually smells floral, which is why perfumers use it and why it shows up naturally in flowers like jasmine. The same compound detected in honey at trace levels is described by tasters as having a “fecal descriptor,” which gives you a sense of how concentration-dependent the perception is.

In your gut, the concentrations are high enough that indole is considered one of the primary contributors to what stool normally smells like. The normal smell of human feces is largely due to indole, which forms from tryptophan that was incompletely digested before reaching the colon.

Why Your Gut Bacteria Control the Smell

Your colon hosts a vast and diverse community of microorganisms, and different species handle tryptophan differently. Some convert it directly to indole. Others push it through the skatole pathway. Still others divert tryptophan into entirely different routes, like the kynurenine pathway or the serotonin pathway, which produce compounds with different (or no) odor profiles.

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The balance of these bacterial populations determines how much indole and skatole end up in your stool on any given day. If the bacteria that favor the indole pathway are thriving, you get more of the mothball smell. If the community shifts toward species that metabolize tryptophan differently, the odor profile changes. This is why the same person can notice the mothball smell some weeks and not others: your gut microbiome is not static. Diet, stress, sleep, illness, and medication all push the microbial community around.

High-Protein Diets and Stronger Odor

Diet is the single biggest lever you have over how much indole and skatole your gut bacteria produce, because both compounds come from protein. Specifically, they come from tryptophan, which is abundant in meat, poultry, eggs, dairy, and certain legumes. The more undigested protein that reaches your colon, the more raw material your bacteria have to ferment into odor-producing compounds.

Research on dietary protein levels has shown that higher protein intake leads to significantly greater production of indoles, phenols, and other volatile compounds, while lower protein intake reduces them.

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This tracks with what gastroenterologists know about high-protein, low-carbohydrate diets: they shift the colonic microbiome toward a more proteolytic (protein-fermenting) profile, increasing not just indoles but also ammonia, hydrogen sulfide, and phenols. All of these compounds contribute to a stronger, more chemically complex stool odor.

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If you recently started a high-protein diet, went heavy on steak or whey protein shakes, or cut back on fiber-rich carbs, that is probably why you are noticing the mothball smell more intensely. The combination of more protein arriving in the colon and fewer fermentable carbohydrates for bacteria to work on instead tips the balance sharply toward indole and skatole production.

How Fiber Blunts the Smell

Fiber does not just speed up transit time through your gut (though it does that too). More importantly for odor, fermentable fibers give your colonic bacteria something else to eat besides protein. When bacteria have access to resistant starch, oligosaccharides, or non-starch polysaccharides, they preferentially ferment those carbohydrates instead, producing short-chain fatty acids like butyrate. Short-chain fatty acids are largely odorless at the concentrations found in stool, and they also happen to be beneficial for the colon lining.

A review of the evidence on colonic protein fermentation found that adding oligosaccharides, resistant starch, and non-starch polysaccharides to the diet can attenuate the increase in protein fermentation byproducts, including the smelly ones.

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In practical terms, that means eating more vegetables, whole grains, legumes, and fruits alongside your protein. You do not necessarily need to eat less protein. You just need to make sure your bacteria have carbohydrate substrates to work with so they are not exclusively fermenting amino acids.

Antibiotics and Sudden Changes in Stool Smell

If the mothball smell appeared suddenly after a course of antibiotics, the explanation is straightforward: antibiotics disrupt the balance of your gut microbiome, sometimes dramatically. They reduce species diversity, alter metabolic activity, and can selectively kill off certain bacterial populations while leaving others untouched.

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Different antibiotics hit different bacterial groups. Doxycycline, for instance, can sharply reduce Bifidobacterium diversity, while clarithromycin decreases populations of Enterobacteria, Bifidobacterium, and Lactobacillus for up to five weeks.

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When certain bacterial populations get wiped out, the surviving species fill the gap. If the survivors happen to be heavy indole producers, you can end up with a temporary spike in mothball-smelling stool that lasts until your microbiome recovers. For most people, the bacterial community bounces back to its baseline within a few weeks after finishing the antibiotic course, though some studies have found effects lasting two to six months.

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Other Medications and Supplements

Antibiotics get the most attention, but they are not the only medications that alter gut microbial metabolism. Proton pump inhibitors (the heartburn drugs you can buy over the counter) change stomach acid levels, which affects how much protein gets fully broken down before reaching the colon. Less complete digestion upstream means more tryptophan available for bacterial fermentation downstream. Metformin, a common diabetes medication, is also known to shift the gut microbiome in ways that change stool odor and consistency.

Supplements matter too. If you are taking tryptophan or 5-HTP supplements for sleep or mood, you are directly increasing the pool of the amino acid that bacteria convert to indole and skatole. High-dose protein supplements, branched-chain amino acid powders, and even large amounts of B vitamins can all shift the chemical profile of your stool in ways that change how it smells.

When the Smell Might Signal Something Worth Investigating

For most people, a mothball-like stool odor is a benign quirk of gut chemistry tied to diet and microbiome composition. But persistent, dramatic changes in stool odor can sometimes reflect underlying gastrointestinal conditions that deserve attention.

Malabsorption syndromes, where your small intestine fails to properly absorb nutrients, send larger quantities of undigested protein and fat into the colon. This extra substrate fuels bacterial fermentation and can produce stool with a distinctly stronger, more chemical smell. Conditions like celiac disease, chronic pancreatitis, and Crohn’s disease all involve some degree of malabsorption. A stool assessment, including macroscopic checks of color, consistency, odor, and mucus, is a standard part of evaluating gastrointestinal disorders in clinical practice.

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The pattern to watch for is not a single unusual-smelling bowel movement. It is a sustained change that persists for weeks, especially if accompanied by other symptoms: unexplained weight loss, chronic diarrhea or loose stools, bloating, visible mucus or blood, or fatigue. Any of these alongside a persistent shift in stool odor is worth bringing up with a doctor, who can run straightforward tests to check for infection, inflammation, or malabsorption.

Clostridioides difficile infection, which sometimes follows antibiotic use, produces a particularly distinctive foul-smelling stool that some people describe as chemical or sweet-putrid. If you have watery diarrhea with an unusual smell after recent antibiotic treatment, that is a specific scenario where prompt medical evaluation matters.

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The Surprising Upside of Indole

Here is where the story gets interesting. The same indole that makes your stool smell like mothballs also plays a genuinely protective role in your gut. Research has shown that indole strengthens the mucosal barrier of the intestinal lining, increases mucin production, and reduces inflammatory signaling. In cell studies, exposure to physiologically relevant amounts of indole increased the expression of genes that reinforce the gut barrier, while simultaneously decreasing markers of inflammation like NF-κB activation and the chemokine IL-8.

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Indole and related compounds derived from intestinal bacteria also activate receptors in your immune system that help maintain the biological barrier of the intestine, exerting anti-inflammatory effects that may be relevant to conditions like inflammatory bowel disease, diabetes, and even central nervous system inflammation.

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So while it is natural to worry when your stool smells strongly chemical, the compound producing that smell is not inherently harmful. In moderate amounts, it is actually a sign that your gut bacteria are doing something useful. The concern arises only when the levels are extremely high (potentially indicating too much protein fermentation and not enough carbohydrate fermentation) or when the odor change accompanies other gastrointestinal symptoms.

Stool Odor as a Frontier in Medical Diagnostics

Researchers are actively working on technology that analyzes the volatile compounds in stool gas as a way to screen for disease. The idea is that different illnesses produce different patterns of volatile organic compounds, and those patterns can be detected by electronic sensor arrays, essentially artificial noses.

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A proof-of-concept study used an electronic nose to analyze fecal gas from patients with colorectal cancer, patients with advanced adenomas, and healthy controls. The device distinguished colorectal cancer from healthy controls with 85% sensitivity and 87% specificity, and could also discriminate advanced adenomas from controls, though with lower accuracy.

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Similar technology has been applied to detecting neonatal sepsis through fecal volatile analysis.

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None of this is clinically available yet for routine screening, and the studies are still early-stage. But the underlying principle is fascinating: the volatile compounds your nose detects when you flush the toilet are genuinely information-rich. They reflect your microbiome composition, your diet, the efficiency of your digestion, and potentially the presence or absence of disease. The mothball smell you notice is your nose picking up on one small piece of that chemical signature. Researchers are trying to build instruments that can read the whole thing.

Practical Steps If the Smell Bothers You

If you are otherwise healthy and the mothball odor is just unpleasant rather than accompanied by worrisome symptoms, dietary changes are the most direct approach:

Add fermentable fiber: Oats, beans, lentils, bananas, onions, garlic, and whole grains all provide substrates that redirect bacterial metabolism away from protein fermentation and toward short-chain fatty acid production.
Moderate protein intake: You do not need to go low-protein, but if you are eating well above what your body needs, some of that excess is reaching your colon undigested. Spreading protein across meals rather than loading it into one sitting also improves small-intestine absorption.
Reduce sulfur-rich foods: While the mothball smell itself is from indole and skatole, sulfur-containing amino acids (found in eggs, cruciferous vegetables, and red meat) contribute hydrogen sulfide to the mix. Cutting back on these can reduce the overall intensity of stool odor even if it does not specifically target the mothball note.
Stay hydrated: Adequate water intake supports normal digestion and transit time, reducing the window during which bacteria ferment protein in the colon.

Probiotics are often suggested for stool odor, but the evidence for a direct effect on indole production is thin. What probiotics can do is help restore microbial diversity after a disruption like antibiotic use, which may indirectly normalize the metabolic balance. If your mothball-smelling stool began after antibiotics, giving your microbiome a few weeks to recover, with a fiber-rich diet to support recolonization, is a reasonable first step before seeking further evaluation.

The Concentration Illusion

One underappreciated factor is that your perception of stool odor is not a reliable measure of what is actually going on chemically. Indole has an extremely low odor detection threshold in humans. The same compound detected in honey samples at concentrations as low as 64 micrograms per kilogram was enough for tasters to register a fecal note.

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Tiny changes in concentration can cross the threshold from “I don’t notice it” to “this smells like a closet full of mothballs.” Your gut chemistry may not have changed much at all. You might simply have tipped from just below your personal detection threshold to just above it. Factors as mundane as how long the stool sat in the toilet bowl before you noticed, how warm the bathroom was (warmth volatilizes more compounds), or even whether you have a mild cold (which dulls smell perception) can all alter what you perceive without anything changing in your actual gut.

This is worth keeping in mind before assuming something is wrong. A one-off mothball-smelling bowel movement is overwhelmingly likely to be meaningless. A pattern that persists for weeks alongside other changes in your health is the signal that warrants investigation.