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Chlamydia trachomatis NAAT

A urine test that looks for the genetic material of the bacteria that cause chlamydia, a common sexually transmitted infection.

AI-verified against cited sources. Awaiting expert reviewAlso called CT NAAT, CT NAALOINC 42931-6

What it is

Chlamydia is a common sexually transmitted infection caused by the bacterium Chlamydia trachomatis. This test is a nucleic acid amplification test, or NAAT. It finds tiny amounts of the bacteria's genetic material in a urine sample, so it can pick up infections that cause no symptoms. The result is printed as detected or not detected. The same kind of test is also done on swabs from the vagina, rectum or throat.

Why it matters

Chlamydia often causes no symptoms, but untreated infection can lead to pelvic inflammatory disease and infertility in women, and less often to pain and swelling in the testicles in men. It can also pass to a baby during birth. It can be cured with antibiotics, so finding it matters. US guidance recommends screening for sexually active women 24 and younger, and for older women at higher risk.

If it’s high

Detected means the test found genetic material from Chlamydia trachomatis in your sample. This usually points to a chlamydia infection, which can be cured with antibiotics. No test is perfect, so your clinician will look at the result along with your symptoms, your partners and how recently you were treated.

Common causes

  • A current chlamydia infection of the urinary or genital tract
  • Getting infected again from a partner who was not treated
  • Testing less than 4 weeks after finishing treatment, when dead bacteria can still be detected
  • Rarely, a false-positive result

What can help

  • Talk with your clinician soon about treatment, since chlamydia can be cured with antibiotics
  • Ask which recent partners should be tested and treated
  • Ask when it is safe to have sex again
  • Ask about retesting in about 3 months

If this applies to you

Chlamydia NAAT means a little more for some people. Open the one that fits you.

Taking HIV PrEP

For people on pills, the CDC suggests chlamydia testing every 3 months for men who have sex with men and transgender women who have sex with men, and every 12 months for heterosexually active women and men, even without symptoms.

Blood tests on HIV PrEP

What can affect your result

  • How the sample is collected: a first-catch sample works best, and a larger or later part of the stream can dilute it
  • Timing after treatment: testing within 4 weeks of finishing treatment can be falsely positive
  • Sample type: vaginal swabs are preferred for women, and first-catch urine is preferred for men
  • Site of infection: urine does not check the rectum or throat
  • Collecting more than the first part of the stream can dilute the sample and lower the chance of detecting the bacteria (Labcorp).
  • Testing less than 4 weeks after finishing treatment can give a false-positive result, because dead bacteria can still be detected (CDC).
  • A urine sample tests the urinary and genital tract only. Infection in the rectum or throat needs a separate swab.
  • For women, a vaginal swab is the preferred sample, and first-catch urine is also accepted (CDC).

A first-catch urine sample is used, which means the first 20-30 mL of the stream. Labcorp asks you not to have urinated for at least 1 hour before collecting it. Follow the instructions your lab gives you. The result shows whether the bacteria's genetic material was present on the day of the sample. After treatment, material from dead bacteria can still be detected for several weeks.

When to talk to a clinician

See a clinician soon if you have burning when you urinate, unusual discharge, pain or swelling in the testicles, or pain in the lower belly, even if a test was negative, because a test only reflects the sample you gave. If you are pregnant and test positive, ask about a recheck about 4 weeks after treatment. Seek urgent care for severe lower belly pain or fever.

Questions you could ask

  • How often should I be screened, given my age and situation?
  • Do I need swabs from other sites as well as a urine test?
  • Which of my recent partners should be tested and treated?
  • When should I be retested?
  • Should I also be tested for other infections?

Questions people ask

Why might I be asked to test again after treatment?

CDC advises retesting about 3 months after treatment because getting infected again is common. A test taken within 4 weeks of finishing treatment can come back positive because of leftover dead bacteria, so it is usually not done that soon.

Can a urine test find chlamydia in the throat or rectum?

No. A urine sample checks the urinary and genital tract. Infection in the throat or rectum is checked with a swab from that site, which your clinician can arrange.

What does a not detected result mean?

It means no chlamydia genetic material was found in that sample. It does not cover infections picked up since the test, and it does not test for other infections such as gonorrhea or HIV.

Show the science and sources

For clinicians and researchers

NAATs amplify Chlamydia trachomatis nucleic acid, for example by transcription-mediated amplification of rRNA (Mayo and Labcorp use Aptima-type assays), and the CDC calls them the most sensitive and recommended tests. Optimal urogenital specimens are first-catch urine for men and vaginal swabs for women, and patient-collected vaginal swabs perform as well as clinician-collected ones. Some NAATs are cleared for rectal and oropharyngeal sites; other sites and specimen types are run as lab-validated tests. The test is qualitative and is not useful for detecting other Chlamydia species (Mayo). NAATs can detect nucleic acid from nonviable organisms, so CDC advises against a test of cure within 4 weeks of finishing therapy, advises retesting about 3 months after treatment, and advises a test of cure about 4 weeks after treatment in pregnancy. Labcorp collects 20-30 mL of first-catch urine, with no urination for at least 1 hour beforehand, because larger volumes may dilute the sample and lower sensitivity. Result LOINC 42931-6 (rRNA, urine) is the code Labcorp prints for this test, and Mayo prints the unspecified-specimen code 43304-5.

LOINC 42931-6 (primary), 43304-5, 6357-8, 16601-7. Specimen: urine.

Sources

  1. Sexually Transmitted Infections Treatment Guidelines, 2021: Chlamydial Infections, Centers for Disease Control and Prevention (2021)
  2. About Chlamydia, Centers for Disease Control and Prevention
  3. Chlamydia and Gonorrhea: Screening, US Preventive Services Task Force (2021)
  4. Chlamydia, NHS
  5. Chlamydia/Gonococcus/Mycoplasma genitalium, NAA, Urine (test 180049), Labcorp (2024)
  6. Chlamydia trachomatis and Neisseria gonorrhoeae, Self-Collect, Amplified RNA, Vaginal (test SCCGV), Mayo Clinic Laboratories
  7. LOINC codes verified with the NLM Clinical Tables LOINC search (e.g. 42931-6), U.S. National Library of Medicine

AI-verified against cited sources. Awaiting expert review. Last reviewed 2026-10-03. How we build and check these pages.

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