The STIs most likely to affect male fertility are chlamydia, gonorrhea, and Mycoplasma genitalium. Each can inflame the urethra and the tubes that carry and mature sperm, and each is frequently silent. Their symptoms overlap so much that only a test tells you which one (if any) you have.
Comparison
| Item | % of cases without symptoms |
|---|---|
| Chlamydia (men) | ~50% |
| Gonorrhea (men) | ~10% |
| Mycoplasma genitalium | ~80% |
The short list of likely causes
When fertility problems in men trace back to an infection, three bacteria come up most often: Chlamydia trachomatis, Neisseria gonorrhoeae, and Mycoplasma genitalium. Each can climb from the urethra into the epididymis (the coiled tube behind each testicle where sperm mature and are stored), causing epididymitis. That inflammation can scar the tube, block sperm transit, and, when it spreads to the testicle itself, threaten sperm production. Most of these infections cause no symptoms while that damage is happening, so screening beats waiting for a sign.
Which STIs cause fertility problems in men
Chlamydia
Chlamydia is caused by the bacterium Chlamydia trachomatis; most US genital infections come from serovars D. K. It's the textbook 'silent' infection, with roughly half of infected men noticing nothing CDC. When symptoms do appear, they usually show up within one to three weeks of exposure and may include discharge or burning on urination. The fertility concern is what happens if it's left untreated and ascends to cause epididymitis: lingering inflammation can scar the duct and impair sperm transport. With no warning signs, a man can carry and pass on chlamydia for months while damage builds. Learn more on our chlamydia overview.
Gonorrhea
Gonorrhea, caused by Neisseria gonorrhoeae, can infect the genitals, rectum, and throat. In men it more often announces itself than chlamydia does: burning when urinating and a white, yellow, or green penile discharge are classic, and less commonly the testicles swell and ache CDC. That swelling is the warning sign of epididymitis, the same fertility-threatening complication chlamydia causes, sometimes with a more dramatic, painful onset. Gonorrhea can be silent too, so feeling clear doesn't make you clear. More detail lives on our gonorrhea page.
Mycoplasma genitalium
Mycoplasma genitalium is a bacterium that lacks a cell wall, so penicillins and cephalosporins, drugs that attack the cell wall, simply don't work against it. It's an emerging cause of urethritis in men. Suspect it when non-gonococcal urethritis (discharge and painful urination) persists or keeps coming back after treatment CDC, 2021. Antibiotic resistance, especially to macrolides, makes it harder to clear and more likely to smolder. It's frequently asymptomatic as well. Diagnosis and drug choice are tricky here, so read why Mycoplasma genitalium.
How to tell them apart
You usually can't, not by symptoms alone. All three can cause urethral discharge and burning, all three can cause epididymitis, and all three are frequently silent. There are loose tendencies: gonorrhea more often produces visibly colored, copious discharge; chlamydia tends to run quieter; and Mycoplasma genitalium is the one to suspect when urethritis keeps returning after a course of antibiotics. But these patterns overlap far too much to settle the question by sight CDC, 2021. A test turns a guess into an answer.
| Feature | Chlamydia | Gonorrhea | Mycoplasma genitalium |
|---|---|---|---|
| Organism | C. trachomatis (serovars D, K) | N. gonorrhoeae | M. genitalium (no cell wall) |
| Typical male symptoms | Often none; discharge/burning if any | Burning, colored discharge; sometimes swollen testicles | Persistent or recurrent non-gonococcal urethritis |
| How often silent | About half of men | Common, but more often symptomatic in men | Frequently asymptomatic |
| Fertility risk | Epididymitis, duct scarring | Epididymitis, duct scarring | Persistent urethritis; under study |
| Recommended test | NAAT | NAAT | FDA-cleared NAAT |
| Antibiotic catch | Standard course | Standard course | Beta-lactams don't work; macrolide resistance common |
How it's tested
For all three, a nucleic acid amplification test (NAAT) is the recommended method: for gonorrhea, NAATs are highly accurate, with sensitivity usually above 90% and specificity around 99% CDC. Mycoplasma genitalium uses an FDA-cleared NAAT on urine or a swab, generally reserved for men with recurrent urethritis. Testing is simpler than people fear: a urine sample, a self-collected swab, or a quick exam depending on what's suspected, often free or low-cost at health departments, Planned Parenthood, and Title X clinics, with results usually back in a few days. See the full how-to and what to bring on our get tested page, and check when to test after exposure so you don't test too early to catch it.
What to do next
If a test comes back positive, all three are treatable with antibiotics, but the right drug differs. Mycoplasma genitalium in particular needs a regimen chosen with resistance in mind, since the common front-line antibiotics fail against it. Don't self-treat or borrow leftover pills. Get the specific infection confirmed, take the full prescribed course, and have your partner(s) treated too so you aren't reinfected. For regimen specifics, follow your clinician's guidance based on your result.
Red flags, when to get seen urgently
- Sudden, severe pain or swelling in one testicle, this can signal epididymitis or a testicular emergency and needs same-day evaluation.
- Fever alongside genital pain or discharge, which suggests the infection is spreading beyond the urethra.
- Discharge or burning that doesn't clear, or comes right back, after you finished a course of antibiotics, a classic clue for Mycoplasma genitalium.
- Blood in the urine or semen, which always warrants a prompt exam.
- A known exposure to a partner diagnosed with an STI, even if you feel completely fine, since silent infections do their damage quietly.
Keep exploring on EasySTD: what STD testing costs, your risk of an STD and Chlamydia testing.