A fishy smell from the penis almost always traces back to bacteria, whether from trapped skin secretions, an infection, or organisms shared with a sexual partner. The groin is warm, moist, and home to a dense community of microbes, so even a small shift in that microbial balance can produce a noticeable odor. The good news is that most causes are straightforward to identify and fix once you know what to look for.
Smegma Buildup Under the Foreskin
If you’re uncircumcised, the most common explanation is smegma, a whitish, paste-like mixture of shed skin cells, oils, and moisture that collects beneath the foreskin. By itself, fresh smegma is mostly odorless. But when it sits undisturbed, bacteria break it down and produce volatile compounds, including some that smell distinctly fishy. The space under the foreskin is essentially a warm pocket with limited airflow, which is exactly the environment anaerobic bacteria thrive in.
Smegma that stays trapped long enough can also lead to localized infection. Researchers studying a condition called cryptitis, an infection of small pocket-like structures near the frenulum, found that smegma trapped in these blind cavities acted as a breeding ground for secondary bacterial infection.1PubMed Central. Etiology, clinical manifestations, and management methods of cryptitis beside the preputial frenulum in men In other words, the buildup itself can escalate from a hygiene issue to a genuine infection if left unaddressed.
The fix here is simple: gently retract the foreskin during a shower and rinse with warm water. Soap is optional and should be mild if used at all, since harsh cleansers can strip the skin’s natural barrier and paradoxically encourage the wrong bacteria to flourish. Daily cleaning is usually enough to prevent smegma from accumulating to the point where it smells.
Anaerobic Bacteria and Balanitis
Sometimes the fishy smell points to something beyond ordinary smegma. The bacterium Gardnerella vaginalis, best known for causing bacterial vaginosis (BV) in women, can also colonize penile skin. When it does, it can cause what’s known as anaerobic balanitis, an inflammation of the glans that comes with a subpreputial discharge described in clinical literature as having a “fishy” smell closely resembling BV odor.2PubMed Central. Penile Inflammatory Skin Disorders and the Preventive Role of Circumcision If the smell comes with redness, irritation, or a thin grayish discharge under the foreskin, this is a likely culprit.
The penile microbiome can be broadly dominated either by typical skin bacteria like Corynebacterium and Staphylococcus, or by the anaerobic bacteria associated with BV.3American Society for Microbiology. Role of the penile microbiome in female sex partner risk of bacterial vaginosis and sexually transmitted infections: a narrative review When the balance tips toward the anaerobic group, the smell follows. Circumcision status, condom use, sexual partners, and antibiotic history all influence which group dominates.
Bacteria Shared Between Sexual Partners
One of the more surprising findings in recent research is how directly BV-associated bacteria are exchanged between sexual partners. A study comparing the microbiota of heterosexual couples found that the penile skin and urethral bacteria of men whose female partners had BV closely matched their partner’s vaginal microbiota, with specific BV-associated species showing up concordantly in both partners.4PubMed Central. Bacterial communities in penile skin, male urethra, and vaginas of heterosexual couples with and without bacterial vaginosis This wasn’t the case for couples where the woman had normal vaginal flora.
This has real practical implications. If your partner has recurrent BV and you notice a fishy smell on your own skin, the two problems are likely connected. Research published in the New England Journal of Medicine found evidence that treating the male partner may help prevent BV from coming back in women.5PubMed. Male-Partner Treatment to Prevent Recurrence of Bacterial Vaginosis A pilot study tested a combination of oral metronidazole and topical clindamycin cream applied to penile skin for seven days, and found the regimen was well tolerated in male participants.6PLOS ONE. Combined oral and topical antimicrobial therapy for male partners of women with bacterial vaginosis: Acceptability, tolerability and impact on the genital microbiota of couples – A pilot study So if the smell persists despite good hygiene, it’s worth bringing up with a doctor, especially if your partner deals with recurring BV.
Sexually Transmitted Infections
Trichomoniasis is the STI most commonly linked to a fishy odor. It’s caused by a parasite called Trichomonas vaginalis, and while people often think of it as a women’s health issue, men get it too. A study of over 2,100 men presenting to emergency departments for STI testing found that about 4.4% tested positive for trichomoniasis. Men who tested positive were more likely to have penile discharge, particularly a clear discharge, on examination.7ScienceDirect. Trichomonas Infection Rates in Males Presenting to the Emergency Department for Sexually Transmitted Infections The infection itself disrupts normal bacterial balance and can produce a fishy or musty odor, especially when discharge is present.
Other STIs like chlamydia and gonorrhea are more commonly associated with a yellow or greenish discharge and a different kind of smell, more pungent than fishy. But any unexplained discharge, pain during urination, or persistent odor after cleaning warrants an STI panel. Trichomoniasis in men is often missed because symptoms can be mild or absent, so many men carry and transmit it without knowing.
Urinary Tract and Prostate Infections
UTIs in men are less common than in women, but when they happen, they can cause urine to take on a strong or foul smell that lingers on the skin. Acute bacterial prostatitis, an infection of the prostate caused by common urinary bacteria, presents with a tender prostate, painful urination, and sometimes foul-smelling discharge. Chronic bacterial prostatitis is subtler, producing recurring pelvic discomfort and recurrent UTIs.8PubMed. Prostatitis and urinary tract infection in men: what’s new; what’s true? These infections are typically caused by gram-negative bacteria and respond to antibiotics, but they need a diagnosis first.
If the fishy smell seems to come from urine rather than the skin itself, or if you notice burning, urgency, or cloudy urine alongside it, a UTI or prostate infection is a reasonable suspicion. Men who are sexually active, especially those having unprotected anal sex, face a higher risk of uncomplicated UTIs.
Diet and Supplements
What you eat and swallow in capsule form can change how your body smells. Fish oil supplements are a well-known offender. Taking fish oil can cause the skin, breath, and urine to carry a fishy odor.9US Pharmacist. Fish Oil: Is It Cardioprotective? The effect is harmless but can be alarming if you don’t connect it to the supplement. Enteric-coated capsules or taking fish oil with meals can reduce the issue, but some people metabolize it in a way that makes the smell persistent regardless.
Beyond supplements, diets heavy in certain fish, asparagus, garlic, and cruciferous vegetables like broccoli and cabbage can temporarily change body odor. These foods contain sulfur compounds or other volatile molecules that get excreted through sweat and urine. The groin, with its high density of sweat glands, picks up these odors faster than other parts of the body. If the smell appeared suddenly and nothing else has changed, consider whether you’ve recently started a new supplement or shifted your diet.
Trimethylaminuria
This one is rare, but it’s worth knowing about because it’s the condition most directly associated with a persistent, whole-body fishy smell. Trimethylaminuria, sometimes called “fish odor syndrome,” is a metabolic disorder where the body can’t properly break down a compound called trimethylamine (TMA). TMA is what gives rotting fish its distinctive smell. In people without the disorder, a liver enzyme converts TMA into an odorless form. In people with the primary inherited form, that enzyme doesn’t work efficiently, so TMA builds up and gets released through sweat, urine, and breath.10PubMed Central. Trimethylaminuria: causes and diagnosis of a socially distressing condition
The smell in trimethylaminuria isn’t limited to the genitals. It’s a body-wide odor that fluctuates with diet, stress, and hormonal changes. Foods rich in choline, like eggs, liver, and certain legumes, tend to make it worse because the gut converts choline into TMA. There’s no cure, but dietary restriction and sometimes low doses of certain antibiotics to reduce gut bacteria that produce TMA can help manage it.11Drug Discovery Today. Treatments of trimethylaminuria: where we are and where we might be heading If you’ve dealt with a fishy body odor since childhood that seems unrelated to hygiene, this is worth discussing with a doctor who can order a urine test for TMA levels.
Sweat, Clothing, and the Groin Microbiome
Even without an infection or metabolic disorder, the groin’s natural microbial community can produce fishy or sour smells under the right conditions. Unpleasant body odor is generally caused by volatile compounds that resident bacteria produce as they metabolize sweat and skin secretions. The specific smell depends on which bacteria dominate and what they have to work with, which in turn depends on diet, the overall composition of your microbiota, and even how well your liver and kidneys are functioning.12PubMed Central. Microbiota and Malodor-Etiology and Management
Tight synthetic underwear makes things worse. Fabrics that don’t breathe trap heat and moisture against the skin, creating an environment where odor-producing bacteria multiply faster. Research on managing skin conditions in fold areas found that choosing breathable, absorbent fabrics reduces microbial colonization, sweat retention, and odor.13Dermatology. Undergarment and Fabric Selection in the Management of Hidradenitis Suppurativa Cotton or moisture-wicking athletic fabrics allow more airflow and pull sweat away from the skin. If you spend long days sitting in polyester boxers, something as basic as switching fabrics might noticeably cut the smell.
Changing underwear daily sounds obvious, but it’s the single most effective clothing-related step. After a gym session or a long hot day, showering and changing into fresh underwear before the sweat dries on your skin prevents the bacterial feast that leads to odor in the first place.
Practical Steps When the Smell Persists
When the smell doesn’t resolve with better hygiene and clothing choices, it’s time to involve a clinician. Here’s a rough order of priorities:
- STI screening: Get tested for trichomoniasis, chlamydia, and gonorrhea, especially if there’s any discharge or burning. Trichomoniasis in men is often asymptomatic and easily missed without a specific test.
- Balanitis evaluation: If there’s redness or irritation under the foreskin along with the smell, a doctor can swab for Gardnerella and other anaerobes and prescribe targeted antibiotics.
- Urine culture: If the odor seems linked to urination, a urine culture can identify a UTI or point toward prostate involvement.
- Partner discussion: If your partner has BV, consider asking your doctor about concurrent treatment. The evidence increasingly supports treating both partners to break the cycle of reinfection.
- Metabolic testing: If the smell is body-wide and has been present for years, a urine test for trimethylamine can rule out or confirm trimethylaminuria.
Avoid the temptation to aggressively scrub the area with antibacterial soap or apply cologne or deodorant to the genitals. These can irritate sensitive skin, disrupt the natural microbial balance, and mask a symptom that a doctor would want to evaluate. Warm water and gentle cleaning are enough for routine hygiene. If there’s an underlying infection, you need antibiotics, not a stronger soap.
When the Smell Might Not Be There
This is a sensitive topic, but it matters enough to mention. Some people are convinced they emit a foul odor when no one around them can detect it. This is a recognized condition called olfactory reference disorder. People with it experience genuine distress and often develop repetitive behaviors like excessive washing or constantly checking for smell. A study of individuals with this condition found that about 35% believed the odor came from their genitals, making it the third most common perceived source after the mouth and armpits.14PubMed Central. Olfactory Reference Syndrome: Demographic and Clinical Features of Imagined Body Odor
Olfactory reference disorder is characterized by the persistent belief that one emits a foul smell, leading to significant distress and social avoidance, often accompanied by repetitive checking and camouflaging behaviors.15PubMed. Olfactory Reference Disorder: Diagnosis, Epidemiology and Management This isn’t the same as anxiety about a real smell. People with the disorder are preoccupied with an odor that others genuinely cannot detect, and the preoccupation can be severe enough to interfere with work, relationships, and daily life.
If you’ve seen multiple doctors who find nothing wrong, no one else can smell what you smell, and the worry has started shaping your daily routines, it’s worth considering this possibility. It responds to certain medications and cognitive-behavioral therapy, and recognizing it can be a significant relief after years of frustration.
Circumcision Status and Odor Risk
Circumcision comes up often in discussions of genital odor, and the connection is real but straightforward. The foreskin creates a sheltered, moist environment where anaerobic bacteria, including BV-associated species, are more likely to colonize. Circumcised men tend to have a penile microbiome dominated by aerobic skin bacteria like Corynebacterium and Staphylococcus, while uncircumcised men are more likely to harbor the anaerobic species that produce fishy-smelling metabolic byproducts.3American Society for Microbiology. Role of the penile microbiome in female sex partner risk of bacterial vaginosis and sexually transmitted infections: a narrative review
This doesn’t mean circumcision is necessary or that being uncircumcised dooms you to a smelly situation. It means uncircumcised men need to be more attentive to daily foreskin hygiene to keep the bacterial balance in check. Most uncircumcised men who clean properly never have a significant odor problem. The foreskin itself isn’t the issue; neglected hygiene in the presence of a foreskin is. And circumcised men aren’t immune to fishy odor from other causes like infections, diet, or partner-transmitted bacteria.