Most men get tested for chlamydia with a simple urine sample. No blood draw, no invasive exam. The test itself takes minutes, and results are typically back within a day. Depending on where you may have been exposed, your provider might also swab the throat or rectum, but for the majority of men, peeing in a cup is all that’s involved.
The Urine Test
The standard chlamydia test for men is a urine sample analyzed with a method called nucleic acid amplification testing (NAAT). This technology detects the genetic material of the bacteria that cause chlamydia, and it’s highly sensitive, catching over 90% of infections with a specificity above 99%. That means false positives are extremely rare.
There’s one important prep step: don’t urinate for at least one hour before giving your sample. Urinating flushes bacteria out of the urethra, which can lead to a false negative. If you’re heading to a clinic or lab for testing, plan accordingly. You’ll provide a “first-catch” sample, meaning the initial stream of urine rather than a midstream sample. This is the opposite of what you’d do for a standard urinalysis, because the goal is to capture any bacteria sitting near the opening of the urethra.
When a Swab Is Used Instead
A urine test is about 87% accurate for detecting chlamydia, while a urethral swab bumps that to roughly 94%. For this reason, providers sometimes use a swab if you have visible discharge or other symptoms suggesting an active infection. The procedure involves inserting a small cotton swab about two centimeters (less than an inch) into the urethra at the tip of the penis and rotating it gently. It’s uncomfortable and can sting briefly, but it’s over in seconds. Like the urine test, you should avoid urinating for at least two hours beforehand.
In practice, most clinics default to the urine test because it’s far more comfortable, widely available, and accurate enough for routine screening. Swabs are typically reserved for situations where a provider wants the highest possible detection rate or needs a discharge culture.
Rectal and Throat Testing
Chlamydia infects wherever it’s transmitted, not just the genitals. If you’ve had unprotected oral or anal sex, a urine test won’t detect an infection in your throat or rectum. Those sites need separate swab tests.
Rectal and throat testing is specifically recommended for men who have sex with men, people who have had contact with a known infected partner, those involved in sex work, and anyone with symptoms at those sites (rectal pain, discharge, or sore throat after oral sex). But any man who has had unprotected exposure at these sites can reasonably request testing based on the circumstances.
For a rectal swab, a provider inserts a small swab a short distance into the anus and rotates it. Throat swabs work exactly like a strep test, with a quick swab of the back of the throat. Both are fast and cause only mild discomfort. NAAT testing on rectal specimens catches around 93% of chlamydia infections. Throat detection is lower, around 69%, because chlamydia is less common and harder to detect in the pharynx. Self-collection of rectal and throat swabs in a clinical setting has been validated as accurate, so some clinics let you swab yourself for privacy and comfort.
When to Test After Exposure
Chlamydia has a window period, meaning there’s a gap between when you’re exposed and when a test can reliably detect the infection. Testing too early produces false negatives.
One week after exposure catches most infections. Two weeks catches nearly all of them. If you test at the one-week mark and get a negative result but still have concerns, retesting at two weeks provides stronger reassurance. Testing the day after a potential exposure is essentially useless, since the bacteria haven’t replicated enough to be detectable.
Who Should Get Screened
Unlike women under 25, who are routinely screened for chlamydia, there’s no blanket screening recommendation for all men. The CDC does recommend annual screening for men who have sex with men, with more frequent testing (every three to six months) for those with multiple partners or ongoing risk behaviors. Testing should cover all relevant anatomical sites, not just urine.
For heterosexual men, testing is situation-driven: a new partner, unprotected sex, symptoms like burning during urination or unusual discharge, or notification that a partner has tested positive. Since chlamydia is often completely asymptomatic in men, waiting for symptoms before testing means many infections go undiagnosed.
Getting Results
Standard lab-processed NAAT results come back in about one day. Some clinics offer rapid tests that return results in 90 minutes or less, though these are less widely available. As of early 2025, the only FDA-authorized at-home chlamydia test (the Visby Medical test) is designed for vaginal swab collection, so there isn’t currently an equivalent home test option for men. Men who want discreet testing can use mail-in services that send a urine collection kit to your home, which you then ship to a lab.
A positive result is straightforward to treat with antibiotics, and your provider will typically recommend that any recent sexual partners get tested and treated as well. Retesting about three months after treatment is standard practice, since reinfection rates are high, particularly if a partner wasn’t treated at the same time.