Chlamydia testing for men is straightforward: in most cases, you simply provide a urine sample. No swabs, no blood draw, no undressing. The test used is called a nucleic acid amplification test (NAAT), which detects the genetic material of the bacteria and is the gold standard recommended by the CDC for diagnosing chlamydia in both symptomatic and asymptomatic men.
The Urine Test
The standard chlamydia test for men involves collecting what’s called a “first catch” urine sample. That means the first part of your urine stream, not a midstream sample like you’d give for a urinalysis. You urinate into a cup, and the lab runs a NAAT on it to look for chlamydia DNA. The whole collection takes under a minute.
This urine-based approach has largely replaced the older method of inserting a thin swab into the urethra (the opening at the tip of the penis). The CDC notes that “overwhelming evidence” shows first-catch urine performs as well as, and sometimes better than, urethral swabs for detecting chlamydia in men. Urethral swabs are still FDA-cleared and occasionally used, but urine is now the default at most clinics and testing sites.
One preparation tip: avoid urinating for at least one to two hours before your test. Urinating too recently can flush bacteria from the urethra and reduce the amount of genetic material in the sample, which could affect accuracy.
Rectal and Throat Swabs
If you’ve had oral or anal sex, a urine test alone won’t catch infections at those sites. Chlamydia can infect the rectum and throat independently of the genitals, so testing needs to happen at the specific location where exposure occurred.
Rectal testing involves a small swab inserted a few centimeters into the rectum. Throat testing uses a swab similar to a strep test. Both use the same NAAT technology as the urine test. Sensitivity is high for rectal chlamydia in men (89% to 93%), though throat detection is somewhat lower (around 69%). The CDC recommends annual rectal chlamydia screening for men who have receptive anal sex.
These swabs are quick and generally cause only brief, mild discomfort. Some clinics allow you to self-collect the rectal swab, which many people prefer.
When to Get Tested After Exposure
Chlamydia won’t show up on a test immediately after exposure. The bacteria need time to multiply enough for the test to detect them. Testing at one week after exposure will catch most infections. Waiting two weeks catches nearly all of them. Testing too early risks a false negative, meaning you could be infected but get a clean result.
If you’re experiencing symptoms like discharge, burning during urination, or pain in the testicles, testing can be done right away regardless of the timeline, since symptoms typically appear only after the bacteria have reached detectable levels. That said, most men with chlamydia have no symptoms at all, which is why testing based on exposure matters.
How Long Results Take
Standard NAAT results are usually ready within one day. Some clinics and urgent care centers offer rapid chlamydia tests that return results in 90 minutes or less, though these aren’t available everywhere. Your provider will typically contact you by phone, patient portal, or text depending on the clinic’s system.
What Happens After a Positive Result
Chlamydia is treated with antibiotics, and the infection clears quickly in most cases. The more important step is what comes after: the CDC recommends retesting three months after treatment. This isn’t to check whether the antibiotics worked (they almost always do) but to catch reinfection, which is common if a sexual partner wasn’t also treated or if there’s new exposure.
You should also notify recent sexual partners so they can get tested. Many health departments offer anonymous partner notification services if you’d rather not do this directly.
Who Should Get Screened Routinely
Unlike women under 25, for whom annual chlamydia screening is a blanket recommendation, routine screening for all young men isn’t currently advised. The evidence on cost-effectiveness just isn’t there yet. However, the CDC does recommend considering screening for men in specific situations: those seen at STI clinics, adolescent health clinics, or correctional facilities, and men who have sex with men. For men who have sex with men, at least annual screening is recommended, with more frequent testing based on risk factors like multiple partners.
Outside of those groups, testing is driven by symptoms, known exposure to a partner with chlamydia, or a new sexual relationship where both partners want to confirm their status.