Chlamydia infects the urethra, rectum, or throat in men, often causing no symptoms at all. About 50% of men with chlamydia never notice anything is wrong, which means the infection can silently spread to partners and cause complications if left untreated for months.
How the Infection Works Inside Your Body
Chlamydia is caused by a bacterium that can only survive and reproduce inside your cells. After exposure, the bacteria enter the cells lining your urethra (the tube you urinate through) in an inactive form. Once inside, they switch to an active state and start consuming the cell’s nutrients to fuel rapid reproduction. Eventually, the cell fills with so many new bacteria that it ruptures and dies, releasing a fresh wave of bacteria that infect neighboring cells. This cycle of invasion, replication, and cell destruction is what drives the inflammation, discharge, and pain that some men experience.
The bacteria can also establish themselves in rectal tissue or the throat, depending on how transmission occurred. In all cases, the infection stays localized at first but can spread deeper into the reproductive tract over time if untreated.
Symptoms You Might Notice
When symptoms do appear, they typically show up one to three weeks after exposure. The most common signs are a discharge from the penis (which can be watery, white, or cloudy), a burning sensation when urinating, and less commonly, pain or swelling in one or both testicles.
But again, half of infected men have zero symptoms. That’s why chlamydia spreads so effectively. You can carry and transmit it for weeks or months without knowing. If you’ve had unprotected sex with a new partner, the absence of symptoms doesn’t mean you’re in the clear.
What Happens If It Goes Untreated
Left alone long enough, chlamydia can move beyond the urethra and cause more serious problems.
Epididymitis
The most common complication in men is epididymitis, an infection of the coiled tube (epididymis) that sits behind each testicle and stores sperm. This causes pain and tenderness on one side of the scrotum, noticeable swelling, and sometimes fluid buildup around the testicle. The inflammation can spread from the epididymis into the testicle itself. Without treatment, epididymitis can lead to chronic pain or, in some cases, affect fertility.
Prostate Infection
Rarely, chlamydia bacteria can reach the prostate gland. Prostatitis causes pain during or after sex, painful urination, lower back pain, and sometimes fever and chills. This is uncommon, but it’s another reason not to let the infection linger.
Reactive Arthritis
In a small number of cases, chlamydia triggers an immune reaction that causes joint inflammation, typically one to four weeks after infection. This reactive arthritis most often hits the knees, ankles, and feet, and can also cause eye redness and irritation, urinary frequency, and low back pain that’s worse in the morning. It’s not common, and it usually resolves on its own over time, but it can be quite uncomfortable while it lasts.
Effects on Fertility
The fertility question worries a lot of men, and the answer is nuanced. The main threat to fertility isn’t the bacteria damaging sperm directly. Research on men with chlamydia-related chronic prostatitis found no significant drop in sperm quality from the infection itself. The real risk comes from structural damage: if epididymitis goes untreated and causes scarring, it can physically block the pathway sperm travel through. Treating chlamydia promptly essentially eliminates this risk.
How Testing Works
Testing for chlamydia in men is straightforward. The preferred method is a nucleic acid amplification test, which detects the bacteria’s genetic material with high accuracy. You’ll either provide a urine sample or have a swab taken from the urethra, rectum, or throat depending on your exposure. Urine testing is more convenient, though swab specimens may be slightly more sensitive for detecting infections in men without symptoms.
Timing matters. If you test too soon after exposure, the bacteria may not have replicated enough to detect. Most infections are detectable after one week. Waiting two weeks catches nearly all cases. Testing before that window can produce a false negative.
Treatment and Recovery
Chlamydia is completely curable with antibiotics. The standard treatment is a seven-day course of oral antibiotics taken twice daily. Most men start feeling better within a few days if they had symptoms, though you should finish the full course regardless.
You should avoid sex for seven days after completing treatment to prevent passing the infection to a partner. Any recent sexual partners need to be tested and treated too, even if they feel fine. Reinfection is common when partners aren’t treated simultaneously. Getting tested again about three months after treatment is a good idea, since reinfection rates are high enough that the CDC recommends it.
One important note: having chlamydia once doesn’t give you any immunity. You can catch it again immediately after being cured if you’re exposed to an infected partner.