Doxycycline is the preferred antibiotic for chlamydia. The standard treatment is 100 mg taken by mouth twice a day for 7 days. This regimen, recommended by the CDC, clears the infection in the vast majority of cases regardless of where in the body the infection is located.
Azithromycin, once the go-to option, is now considered a backup. Here’s what you need to know about both options, how they compare, and what to expect during treatment.
Doxycycline: The First Choice
Doxycycline is a tetracycline antibiotic that works by stopping the chlamydia bacteria from producing the proteins they need to survive. The full course takes 7 days, with one pill in the morning and one in the evening. You need to finish all 14 doses even if symptoms clear up sooner.
The reason doxycycline replaced azithromycin as the top recommendation comes down to cure rates. A meta-analysis and Cochrane systematic review of randomized clinical trials found that treatment failure was higher with azithromycin than doxycycline, particularly in men. The gap is even wider for rectal chlamydia: one randomized trial reported a 100% cure rate with doxycycline compared to just 74% with azithromycin.
That rectal infection detail matters more than you might think. Chlamydia can be present in the rectum even in people who don’t report anal sex, especially in women. When a rectal infection goes untreated, it can reinfect the urogenital tract on its own through a process called autoinoculation. Doxycycline handles both sites at once, which is a major advantage.
Tips for Taking Doxycycline
Doxycycline can make your skin noticeably more sensitive to sunlight. Even brief exposure may cause rash, redness, or a severe sunburn. Try to avoid direct sun between 10 a.m. and 3 p.m. while on the medication, and wear sunscreen if you’ll be outside. Some formulations should be taken on an empty stomach (at least one hour before or two hours after eating), though this varies by brand. Check the label or ask your pharmacist whether yours should be taken with food or without.
Azithromycin: The Alternative
Azithromycin is a single-dose treatment: one gram taken all at once. Its biggest selling point is convenience. You take one dose and you’re done, which eliminates any concern about forgetting pills over a week-long course.
For urogenital chlamydia in women, azithromycin still works well. The issue is that it performs significantly worse against rectal infections, and since rectal chlamydia often coexists silently alongside a urogenital infection, a single dose of azithromycin can leave bacteria behind. That’s why the CDC now reserves azithromycin for situations where completing the full 7-day doxycycline course is genuinely unlikely. If you do receive azithromycin, your provider may want to do a follow-up test to confirm the infection has cleared.
Treatment During Pregnancy
Doxycycline is not safe during pregnancy because tetracycline antibiotics can affect fetal bone and tooth development. Pregnant individuals are typically treated with azithromycin or amoxicillin instead. Because these alternatives have somewhat lower efficacy at certain infection sites, a test-of-cure after treatment is especially important during pregnancy to make sure the infection is fully resolved.
What to Expect After Treatment
Chlamydia symptoms, if you had any, generally start improving within a few days of beginning antibiotics. Many people with chlamydia have no symptoms at all, so treatment may feel uneventful. You should avoid sex for 7 days after starting doxycycline (which means until you’ve finished the full course) or for 7 days after taking a single dose of azithromycin. Having sex before that window closes risks passing the infection to a partner or getting reinfected yourself.
Retesting is recommended about 3 months after treatment. This isn’t because the antibiotics failed; it’s to catch reinfection, which is common. Testing too soon after treatment (within a few weeks) can produce a false positive because dead bacterial DNA may still be detectable.
Your Partner Needs Treatment Too
Chlamydia treatment only works long-term if your sexual partners are also treated. Otherwise, you’ll likely get reinfected the next time you have sex with them. In many states, your provider can use a practice called Expedited Partner Therapy, where they write a prescription or provide medication for your partner without needing to examine them first. This is particularly useful when a partner can’t easily get to a clinic on their own.
Any partner you’ve had sex with in the 60 days before your diagnosis (or your most recent partner if it’s been longer) should be treated. They should also avoid sex for 7 days after their own treatment begins.
Why Chlamydia Doesn’t Go Away on Its Own
Unlike some infections your immune system can eventually clear, chlamydia tends to persist without antibiotics. Untreated chlamydia in women can spread to the uterus and fallopian tubes, causing pelvic inflammatory disease, chronic pelvic pain, and fertility problems. In men, it can cause painful swelling in the tube that carries sperm, which can also affect fertility. These complications develop silently over months, which is why treatment matters even when you feel fine.
The good news is that chlamydia responds reliably to antibiotics. Resistance to doxycycline remains extremely rare, so when the full course is completed, the infection clears. Reinfection from an untreated partner is by far the most common reason people test positive again after treatment.