Rectal chlamydia is an infection of the rectum and anal canal caused by the bacterium Chlamydia trachomatis, usually acquired through receptive anal sex. It's frequently silent, but can cause rectal pain, discharge, or bleeding. A self-collected rectal swab tested by NAAT detects it, and a short course of doxycycline cures it.
urine or swab
after exposure
100 mg 2×/day, 7 days
catches reinfection
| Item | Value |
|---|---|
| Test method | NAAT — urine or swab |
| When to test | ~2 wks — after exposure |
| Treatment | doxycycline — 100 mg 2×/day, 7 days |
| Retest | 3 mo — catches reinfection |
The essentials: what rectal chlamydia is
Rectal chlamydia is the same organism behind genital chlamydia, Chlamydia trachomatis, with most US infections caused by serovars D–K CDC. The bacteria infect the lining of the rectum and anal canal, typically after receptive anal sex, though it can also reach the rectum from genital secretions. Chlamydia is the most commonly reported bacterial STI in the US, with about 1.65 million reported cases in 2023 (492 per 100,000), a rate that's held roughly flat across 2020–2023 CDC AtlasPlus, 2023. Burden varies sharply. Washington DC (1,228 per 100,000), Louisiana, and Mississippi sit at more than double the national rate.
Chlamydia is curable with the right antibiotic. Because urine and standard genital tests don't sample the rectum, a rectal infection can persist undetected unless the rectum itself is swabbed, so site-specific testing matters here.
Symptoms of rectal chlamydia
Most rectal chlamydia causes no symptoms at all. Chlamydia is a 'silent' infection overall, with roughly three quarters of infected women and half of infected men noticing nothing, and the rectum is no exception. When symptoms do show up, they reflect proctitis, inflammation of the rectal lining, and include:
- Rectal pain, including a deep or aching discomfort during bowel movements.
- Anal or rectal discharge, sometimes mucus-like.
- Rectal bleeding or blood-streaked stool.
- A sensation of needing to pass stool when the rectum is empty (tenesmus).
Because so many infections are quiet, symptoms are a poor guide to who's infected. If you have receptive anal sex, the only reliable way to know is to test the site rather than wait for pain or discharge that may never come.
When it's LGV, not ordinary rectal chlamydia
A more aggressive form deserves a flag. Lymphogranuloma venereum (LGV) is caused by invasive C. trachomatis serovars L1, L2, and L3, with the highest burden in men who have sex with men CDC. It usually presents as proctocolitis, with mucoid or bloody rectal discharge, significant anal pain, and tenesmus, and tends to be more severe than the serovar D–K infection. LGV needs a longer antibiotic course, so a clinician evaluating notable rectal symptoms in an at-risk person will consider it specifically.
Testing for rectal chlamydia
The recommended and most sensitive test is a nucleic acid amplification test (NAAT), which detects the bacterium's genetic material and works on genital and extragenital sites alike CDC STI Treatment Guidelines, 2021. For the rectum, that means a rectal swab. A urine sample or a genital swab will miss a rectal infection entirely, because each NAAT only detects what was sampled. Specimen options across the body include first-catch urine, endocervical, vaginal, urethral, rectal, and pharyngeal swabs.
A rectal swab is brief, and many clinics let you self-collect it, which most people find easier and less awkward than a clinician-collected sample. There's no blood draw and no urethral swab. Results are often back within a few days, sometimes texted to you. For the full walkthrough, see our guide to chlamydia testing & diagnosis, and you can get tested at a clinic or with an at-home kit.
The most common testing mistake is going in the morning after sex. A NAAT is most reliable roughly two weeks after exposure, so a test done too early can come back negative even when infection is taking hold. If you've had a recent exposure, check our note on when to test after exposure before you book.
Who should ask for a rectal swab
Screening guidance is asymmetric by design. The USPSTF gives a Grade B recommendation to screen sexually active women 24 and under, but an I-statement (insufficient evidence) for screening men, because the major complications, pelvic inflammatory disease and infertility, fall on women USPSTF. None of that captures the rectum directly, so if you have receptive anal sex, say so and request a rectal swab. The test is only done if the site is sampled, and clinics won't know to add it unless you mention your exposures.
Treatment for rectal chlamydia
The first-line treatment is doxycycline, 100 mg by mouth twice daily for 7 days CDC. Doxycycline clears rectal infection far more reliably than the old single-dose option. A randomized trial found doxycycline cured 100% of rectal chlamydia versus 74% with azithromycin RCT, Clin Infect Dis, and that gap is the main reason the 2021 guidelines made doxycycline first-line and downgraded azithromycin from co-equal status.
Azithromycin (1 g as a single dose) and levofloxacin (500 mg once daily for 7 days) remain alternatives, but for a known rectal infection, doxycycline is the clear winner. If you're weighing the two, our breakdown of azithromycin vs doxycycline for chlamydia explains the trade-offs in detail.
| Regimen | How it's taken | Notes for rectal infection |
|---|---|---|
| Doxycycline 100 mg | Twice daily, 7 days | First-line; best rectal cure rate |
| Azithromycin 1 g | Single dose | Alternative; lower rectal cure in trials |
| Levofloxacin 500 mg | Once daily, 7 days | Alternative |
| Doxycycline 100 mg (LGV) | Twice daily, 21 days | Longer course if LGV is suspected/confirmed |
To make the 7-day course work: take doxycycline with food to settle your stomach, and avoid strong sun exposure since it can make you sunburn more easily. If LGV is diagnosed, the course extends to doxycycline 100 mg twice daily for 21 days, with azithromycin or erythromycin as alternatives. For everything on the recovery side, see our full guide to chlamydia treatment.
Partners and follow-up
Treating only yourself sets up 'ping-pong' reinfection. Partners from the prior 60 days should be referred, tested, and presumptively treated. Expedited partner therapy (EPT), giving you medication or a prescription to hand to a partner, is permissible in most US states but not all, so verify local rules. In a landmark randomized trial it cut persistent or repeat infection Golden et al., NEJM. Abstain from sex for 7 days after single-dose therapy, or until you finish the 7-day course.
Put a retest on your calendar for about 3 months after treatment to catch reinfection. It's not a test-of-cure, which isn't advised for non-pregnant people unless your adherence is in question, symptoms persist, or reinfection is suspected.
Preventing rectal chlamydia
Condoms used correctly every time lower risk, and a long-term mutually monogamous relationship with a tested partner removes it. Because most infections are silent, condoms alone don't carry the load. Routine screening and treating partners do the real work of breaking transmission chains.
For eligible people there's also DoxyPEP: a single 200 mg dose of doxycycline taken within 72 hours of sex, which reduces chlamydia by more than 70% CDC DoxyPEP. The CDC offers it to gay and bisexual men and transgender women who've had a bacterial STI in the past 12 months CDC, 2024 MMWR. It's a tool worth discussing with a clinician if you fit that group.
When to see a clinician
Book a visit if you notice rectal pain, discharge, or bleeding, especially with the urge to pass stool when the rectum is empty, since those point toward proctitis and, in at-risk people, possible LGV that needs a longer course. Also seek care if a partner tests positive, if you've had a recent exposure you want cleared, or simply because you have receptive anal sex and haven't had a rectal swab. Testing positive is routine and curable; clinics handle it every day. In many states you can notify partners anonymously.