Chlamydia is treated with antibiotics, and the current first-line recommendation is doxycycline, taken twice a day for seven days. This replaced the older go-to option, a single dose of azithromycin, after research showed doxycycline has a higher cure rate. With the right antibiotic and a full course of treatment, chlamydia clears up reliably.
Doxycycline: The Preferred Treatment
Doxycycline is now the standard antibiotic for chlamydia. You take it twice daily for a full week. It works by blocking the bacteria’s ability to make the proteins they need to survive and multiply, effectively stopping the infection in its tracks.
The shift to doxycycline as the top choice happened because head-to-head comparisons showed azithromycin had a higher treatment failure rate, particularly in men. For rectal chlamydia infections, the difference is dramatic: one randomized trial found doxycycline cured 100% of rectal infections compared to just 74% for azithromycin. Multiple observational studies confirmed the same pattern for rectal infections in both men and women.
Why Azithromycin Is No Longer First Choice
For years, azithromycin was the default chlamydia treatment because of its convenience. You took a single dose and were done. That simplicity made it appealing, especially for patients who might struggle to complete a week-long course of pills. But convenience came at a cost: systematic reviews and meta-analyses of clinical trials consistently found that azithromycin led to more treatment failures than doxycycline for urogenital chlamydia in men.
Azithromycin may still be used in certain situations where doxycycline isn’t an option, but it’s no longer considered the best choice for most people.
What to Expect During Treatment
Doxycycline is generally well tolerated, but it does come with a few things to keep in mind. The most common side effect is stomach upset, including nausea. Taking it with food and a full glass of water helps reduce this. Avoid lying down for at least 30 minutes after swallowing the pill, since doxycycline can irritate your esophagus if it doesn’t move all the way to your stomach.
Doxycycline also makes your skin more sensitive to sunlight. You’ll burn faster and more easily during the week you’re on it, so wear sunscreen or limit your sun exposure. Dairy products, calcium supplements, and antacids can interfere with how well doxycycline is absorbed, so space those out by a couple of hours from your dose.
The most important thing is finishing all seven days, even if your symptoms clear up before then. Stopping early gives the bacteria a chance to survive and bounce back.
Treatment During Pregnancy
Doxycycline is not safe during pregnancy because it can affect fetal bone and tooth development. Pregnant patients are typically treated with azithromycin or amoxicillin instead. If you’re pregnant or think you might be, let your provider know before starting treatment so they can choose an appropriate antibiotic.
Where the Infection Is Matters
Chlamydia doesn’t only infect the genitals. It can also occur in the rectum or throat, and where the infection is located affects how well certain antibiotics work. Doxycycline is especially important for rectal chlamydia, where azithromycin’s cure rate drops significantly. If you’ve been tested at multiple body sites and have a rectal infection, doxycycline is the clear choice.
Avoiding Sex During Treatment
You need to wait at least seven days after both you and your partner finish treatment before having sex again. Having sex too soon, even with a condom, risks passing the infection back and forth. This waiting period applies regardless of which antibiotic you or your partner were prescribed.
Getting Your Partner Treated
Chlamydia treatment only works long-term if your sexual partner is also treated. Otherwise, you’ll likely get reinfected the next time you have sex. In many states, your healthcare provider can write a prescription for your partner without needing to examine them first. This is called Expedited Partner Therapy, and the CDC supports it as a practical way to break the cycle of reinfection, particularly for male partners of women diagnosed with chlamydia.
That said, the ideal scenario is for your partner to get their own exam and testing, since they could have additional infections that need attention. EPT is a backup option when your partner can’t or won’t come in.
Retesting After Treatment
Even after successful treatment, the CDC recommends retesting three months later. This isn’t because the medication failed. It’s to catch reinfection, which is common. People who’ve had chlamydia once are at higher risk of getting it again, often from an untreated partner or a new exposure. That three-month retest is one of the most effective tools for catching a repeat infection early, before it causes complications like pelvic inflammatory disease or fertility problems.