Chlamydia is the most commonly reported bacterial sexually transmitted infection in the United States, with over 564,000 cases reported among men in 2024 alone. In men, it primarily infects the urethra, causing painful urination and discharge, but many infections produce no symptoms at all. Left untreated, it can spread deeper into the reproductive tract and, in rare cases, trigger problems in the joints and eyes.
Many Men Have No Symptoms
One of the biggest challenges with chlamydia in men is that the infection is often silent. Many men carry the bacteria without ever noticing anything wrong, which means they can unknowingly pass it to sexual partners for weeks or months. When symptoms do appear, the most common ones are a burning sensation during urination and an unusual discharge from the penis. Some men also develop pain or tenderness in one or both testicles.
The lack of obvious symptoms is a major reason chlamydia spreads so easily. If you’ve had unprotected sex with a new or untested partner, you can’t rely on feeling fine as evidence that you’re in the clear.
How the Infection Takes Hold
The bacterium that causes chlamydia targets the thin layer of cells lining the urethra (and, in the case of anal sex, the rectum). It exists in two forms: a small, hardy form that’s built to survive outside cells and latch onto new ones, and an active form that reproduces inside your cells. Once the hardy form attaches to a cell, it’s absorbed inside and shifts into its active, reproducing mode. It hijacks the cell’s nutrients to make copies of itself, eventually producing so many new bacteria that the cell bursts open and dies. The released bacteria then infect neighboring cells, and the cycle repeats.
This process triggers inflammation, which is what causes the burning, swelling, and discharge that some men experience. Because the bacteria need living cells to reproduce, the infection stays localized to the tissues it can colonize, primarily the urinary and genital tract.
Epididymitis: The Main Complication
When chlamydia goes untreated, the bacteria can travel from the urethra up through the reproductive tract to the epididymis, the coiled tube behind each testicle where sperm mature. This causes a condition called epididymitis, which typically shows up as pain and swelling on one side of the scrotum. The swelling usually starts at the lower part of the epididymis and can spread to the rest of the structure and the testicle itself. The spermatic cord, which connects the testicle to the rest of the body, often becomes tender and swollen too.
Epididymitis can also cause fluid buildup around the testicle, known as a hydrocele, which adds to the swelling. If it becomes severe or recurrent, it has the potential to affect fertility by damaging the tubes that transport sperm, though this outcome is uncommon with proper treatment.
Links to Prostatitis and Fertility
There’s growing evidence that chlamydia may play a role in chronic prostatitis, a condition involving persistent inflammation of the prostate gland that causes pelvic pain, difficulty urinating, and sexual discomfort. Researchers believe the bacteria can climb from the urethra into the prostate through the connecting ducts. One study of men with chronic prostatitis detected chlamydia in 10% of their semen samples, and about a third showed immune markers in their seminal fluid suggesting a past or ongoing chlamydial infection.
The connection between chlamydia and long-term sperm damage is still debated. That same study found that chlamydia in the prostate didn’t seriously compromise sperm quality, but chronic inflammation in the reproductive tract is generally not favorable for fertility. Treating the infection early avoids this concern entirely.
Reactive Arthritis: A Rare but Serious Effect
In a small number of men, chlamydia triggers a condition called reactive arthritis (formerly known as Reiter syndrome), where the immune system overreacts to the infection and attacks the body’s own tissues. This isn’t common, but when it happens, it typically produces three categories of symptoms: joint pain and stiffness (especially in the knees, ankles, feet, and lower back), urinary problems like burning or frequent urination, and eye inflammation resembling pink eye, sometimes with blurred vision.
Reactive arthritis usually resolves on its own over time, but it can last weeks to months and cause significant discomfort. It tends to occur after the initial infection, so you might not immediately connect the joint pain to a sexual exposure that happened weeks earlier.
Testing: What to Know About Timing
Chlamydia testing for men is straightforward. The standard approach is a urine sample analyzed with a highly sensitive molecular test that detects the bacteria’s genetic material. These tests have specificity above 99%, meaning false positives are extremely rare. Sensitivity is generally strong, though urine-based testing can be slightly less sensitive in men without symptoms compared to a urethral swab.
Timing matters. If you test too soon after exposure, the bacteria may not have multiplied enough to be detected. A test taken one week after potential exposure will catch most infections. Waiting two weeks catches nearly all of them. Testing before the one-week mark risks a false negative, which could give you a misleading sense of security.
Treatment Is Simple and Effective
Uncomplicated chlamydia in men is treated with a seven-day course of an antibiotic taken twice daily. This is the current first-line recommendation from the CDC, replacing what was previously a single-dose option. The single-dose alternative is still available but is now considered a backup. A once-daily delayed-release formulation also exists and is equally effective, which can make the week of treatment easier to manage.
You should avoid sexual contact until you’ve completed the full course and any current partners have been tested and treated. Reinfection is common because treating yourself doesn’t protect you if your partner still carries the bacteria. The CDC recommends retesting about three months after treatment to catch reinfections early.
Rectal and Throat Infections
Chlamydia doesn’t only affect the urethra. Men who have receptive anal sex can develop a rectal infection, which may cause rectal pain, discharge, or bleeding, though it’s also frequently asymptomatic. Throat infections from oral sex are possible but less common and rarely cause noticeable symptoms. If you’re sexually active in ways that go beyond vaginal or penile contact, mention this to your provider so the right sites get tested. A urine test alone won’t detect infections in the rectum or throat.