Chlamydial urethritis is inflammation of the urethra caused by Chlamydia trachomatis, and in men it can spread beyond the urethra to cause painful complications: epididymitis (inflammation of the coiled tube behind the testicle), reactive arthritis, and proctitis among them. Antibiotics cure it. But most male infections cause no symptoms, so untreated cases keep transmission going.
Key figures
- Test method
- NAAT
- urine or swab
- When to test
- ~2 wks
- after exposure
- Treatment
- doxycycline
- 100 mg 2×/day, 7 days
- Retest
- 3 mo
- catches reinfection
| Item | Value |
|---|---|
| Test method | NAAT: urine or swab |
| When to test | ~2 wks: after exposure |
| Treatment | doxycycline: 100 mg 2×/day, 7 days |
| Retest | 3 mo: catches reinfection |
The essentials
Chlamydia is the most commonly reported bacterial sexually transmitted infection in the United States, roughly 1.65 million reported cases in 2023, about 492 per 100,000 people CDC, 2023. Counts have stayed roughly flat across recent years, though provisional data showed a decline in the most recent reporting period CDC. It's also concentrated geographically: Washington DC, Louisiana, and Mississippi report rates more than double the national figure.
Most US genital infections come from C. trachomatis serovars D through K. The bacterium infects the lining of the urethra, where it triggers the inflammation men feel as burning or notice as discharge. Globally, an estimated 128.5 million new infections occurred among adults aged 15 to 49 in 2020 WHO. Clinicians call chlamydia a 'silent' infection because about half of infected men have no symptoms at all. That silence lets complications sneak up, so it's worth screening before any sign appears.
Chlamydia and gonorrhea often look identical at the urethra and frequently travel together; if you want to understand how they differ in testing and treatment, see chlamydia vs gonorrhea.
Symptoms of chlamydial urethritis in men
When symptoms do appear in men, the classic triad is penile discharge, burning on urination, and irritation at the tip of the penis. The discharge is often clear or cloudy rather than thick and yellow, and it can be subtle, sometimes nothing more than a single drop noticed first thing in the morning before urinating. Burning or itching right at the penile opening is common, and some men also develop testicular pain or swelling.
That testicular symptom warns you the infection has climbed. The painful complications:
- Epididymitis: inflammation of the epididymis, the coiled tube behind each testicle that stores and carries sperm. It causes one-sided testicular pain, swelling, and tenderness, and untreated infection here can scar the duct and affect fertility.
- Reactive arthritis: an immune reaction triggered by the infection that can inflame the joints, eyes, and urethra together. It's painful, can outlast the infection itself, and is more common in men than women.
- Proctitis: inflammation of the rectum in men who have receptive anal sex, causing rectal pain, discharge, or bleeding. Rectal infection is frequently silent, so it can persist undiagnosed.
Throat (pharyngeal) infections are typically asymptomatic and usually found only on testing. The absence of symptoms tells you nothing about whether you're infected, and waiting for pain leaves the infection unchecked.
How chlamydia is tested
The recommended method is a nucleic acid amplification test (NAAT), which detects the bacterium's genetic material and is the most sensitive assay available, with specificity that rivals old-fashioned cell culture without the hassle NIH. For men, the preferred specimen is a first-catch urine sample (the first part of the stream, ideally after holding urine about an hour), which means no blood draw and no uncomfortable urethral swab. Rectal and pharyngeal swabs are used when those sites are exposed.
In practice, testing is quick and low-friction: you provide the urine cup or, for at-home kits, a self-collected swab, and results are often back within a day to a few days, sometimes by text. The most common mistake is testing too soon. A NAAT is most reliable about two weeks after exposure, so a negative result the morning after a hookup can be falsely reassuring, read more on when to test after exposure before you book.
Cost is rarely the barrier people fear. Testing is free or low-cost at Planned Parenthood, health departments, and Title X clinics; at-home kits run roughly $50–150; and it's often $0 with insurance. If you're ready, here's how to get tested.
One note on screening philosophy from an epidemiologist's seat: the USPSTF gives a Grade B recommendation to screen all sexually active women 24 and younger, but issues an I-statement, insufficient evidence, for screening men USPSTF. That asymmetry isn't because men can't be harmed; it's because the population-level complication burden of pelvic inflammatory disease and infertility falls on women. For an individual man with symptoms or a known exposure, testing is clearly worthwhile.
Treatment: what cures it
Chlamydia is curable. The preferred regimen in the 2021 CDC guidelines is doxycycline 100 mg orally twice daily for 7 days CDC, 2021. Azithromycin 1 g as a single dose and levofloxacin 500 mg once daily for 7 days are listed as alternatives.
Why the shift away from the convenient single dose? Microbiologic treatment failure in men was higher with azithromycin than with doxycycline, and the difference is stark for rectal infection: a randomized trial found 100% cure with doxycycline versus 74% with azithromycin RCT. That finding drove guidelines to make the 7-day doxycycline course first-line.
| Regimen | Dose & duration | Role |
|---|---|---|
| Doxycycline | 100 mg orally twice daily for 7 days | Preferred; best for rectal infection |
| Azithromycin | 1 g orally, single dose | Alternative; preferred in pregnancy |
| Levofloxacin | 500 mg orally once daily for 7 days | Alternative |
Practical reality of the doxycycline course: take it with food to ease nausea, avoid strong sun because the drug increases photosensitivity, and finish all seven days even after symptoms fade. Doxycycline is contraindicated in pregnancy, where azithromycin 1 g as a single dose is the recommended option CDC, 2021.
Partners need treating too. Anyone you've had sex with in the prior 60 days should be referred for testing and treatment, ideally presumptively. Abstain from sex for seven days after single-dose therapy or until the full 7-day course is complete. Expedited partner therapy, where you carry medication to a partner, measurably cuts persistent and repeat infection, with the largest benefit seen for gonorrhea (3% vs 11%) in a landmark trial CDC. EPT is permissible in most but not all states, so verify your local status. Many clinics also let you notify partners anonymously.
Don't skip the retest. CDC recommends retesting everyone treated for chlamydia about three months later, regardless of whether you think your partner was treated CDC. This catches reinfection; it is not a test-of-cure. A true test-of-cure isn't advised for non-pregnant people unless adherence is doubtful, symptoms persist, or reinfection is suspected. Learn how to time the follow-up at chlamydia reinfection.
A note on LGV
Lymphogranuloma venereum (LGV) is caused by the more invasive C. trachomatis serovars L1, L2, and L3, with the highest burden in men who have sex with men. It usually presents as proctocolitis: mucoid or bloody rectal discharge, anal pain, and tenesmus (the painful urge to pass stool when little comes). LGV needs a longer course: doxycycline 100 mg twice daily for 21 days, with partners from the prior 60 days given a shorter presumptive course CDC.
Prevention that actually works
Condoms used correctly every time reduce transmission, and a long-term mutually monogamous relationship with a tested partner is protective. But since most infections are silent, the measures that move the needle at a population level are routine screening and treating partners. For the full strategy, see preventing chlamydia.
There's also a newer tool. In 2024, CDC issued its first guidelines recommending doxycycline postexposure prophylaxis. DoxyPEP, a single 200 mg dose of doxycycline taken within 72 hours after sex CDC. Across three large randomized trials, it reduced chlamydia and syphilis infections by more than 70% and gonorrhea by roughly half CDC, 2024. It's offered to men who have sex with men and transgender women who've had a bacterial STI in the prior 12 months: not a universal measure, but a real option for eligible people.
When to see a clinician
See a clinician promptly if you have penile discharge, burning on urination, or testicular pain or swelling, which can signal epididymitis. Men who also notice changes in their erections can gauge them separately with the IIEF-5 erectile-function self-check. Get tested after a known exposure or a new partner even without symptoms, and don't be talked out of it by an early negative taken too soon. If you've been treated, put the three-month retest in your calendar.
Testing positive is routine and curable. Clinics handle chlamydia every day, and getting treated quickly is what protects your fertility and your partners.
Keep exploring on EasySTD: when to re-test, confidential testing by state and Chlamydia testing.