Explanation

Chlamydia trachomatis PCR (urine): what is measured?

Chlamydia is an STI caused by the bacterium Chlamydia trachomatis. The PCR looks for genetic material of the bacterium in the first portion of urine (first-void urine). That first part of the stream contains the most material from the urethra; that is why you collect only that part and, according to the kit instructions, do not urinate for at least 1 hour beforehand. The result only says something about the urethra: an infection in the anus or throat is not found with urine.

What can it detect?

A current chlamydia infection of the urethra, even if it causes no symptoms
In men: a possible cause of pain when urinating, discharge from the penis or pain in the scrotum

Result

What does the result mean?

Positive result

A positive result means that genetic material of the chlamydia bacterium was found. This usually fits a current infection, even if you have no symptoms: up to 9 in 10 women and about half of men notice nothing. Chlamydia can be treated well with antibiotics. Without treatment, the infection often clears up on its own over time, but in women it can sometimes spread upward and cause inflammation of the womb and fallopian tubes; according to the LCI guideline (RIVM), the chance of permanent infertility after chlamydia is small (0.5 to 1 percent). In men, chlamydia rarely causes complications; sometimes an inflammation of the epididymis or prostate develops.

Negative result

A negative result means that no chlamydia was found in the urine. According to the LCI guideline (RIVM), the test is reliable from 2 weeks after the last risky sexual contact; within those 2 weeks, an infection can still be missed. The result only applies to the urethra at the time of sample collection and does not rule out an infection in the anus or throat. If your symptoms continue, there may be another cause.

After an abnormal result

With a positive result, the GP usually prescribes a course of antibiotics and advises no sex for a week; the GP discusses warning sexual partners and testing for other STIs such as gonorrhea, HIV and syphilis. A test of cure after treatment is usually not needed, except during pregnancy or with persistent symptoms. Individual cases of chlamydia are not notifiable.

Reliability

How reliable is the test?

According to the LCI guideline (RIVM) and the Multidisciplinary Guideline on STIs, the PCR (a NAAT: a test that multiplies genetic material of the bacterium and so detects it) is the standard test for chlamydia, with high sensitivity and specificity on urine and self-collected swabs. For men, first-void urine is the usual sample; in women, a vaginal swab is more sensitive than urine. According to the LCI guideline, a negative result is reliable from 2 weeks after the risky sexual contact. Because the test detects genetic material, it can still be positive for up to a few weeks after treatment.

What can affect the result?

Less than 2 weeks after the risky sexual contact, the test can miss an infection.
If you urinated less than 1 hour before the sample collection, or collect more than the first part of the stream, the sample is diluted and the test can miss an infection.
Urine only tests the urethra. In men who have sex with men, chlamydia is often only in the anus; that infection is missed with urine. For women, urine is less sensitive than a vaginal swab.
Within 3 weeks after treatment, the test can be positive due to leftover genetic material, even if the infection is gone.

Preparation

Collect the urine when you have not passed urine for at least 1 hour.
Collect only the first part of the stream, not the middle part.

Who it is for

Who is the test useful for?

Useful for

Useful for men (and other people with a penis) with symptoms that may fit chlamydia, such as pain when urinating or discharge from the penis, and for anyone whose sexual partner has chlamydia. Thuisarts also mentions sex without a condom with a new or changing partner as a reason to test, from 2 weeks after the contact. The benefit of testing without symptoms is uncertain, because many infections clear up on their own; since January 2025, the GGD (municipal public health service) only tests when there are symptoms or when a partner with symptoms has chlamydia. For women, a vaginal swab is the better choice, and after anal sex a separate swab of the anus is needed.

How common is it?

Chlamydia is the most common bacterial STI in the Netherlands. In 2024, the sexual health centers of the GGD (municipal public health service) found chlamydia in 20,174 people, two thirds of whom had no symptoms; GPs made the diagnosis about 43,000 times in 2023. Chlamydia is most common in young people under 25.

RIVM (GGD sexual health centers 2024, GPs 2023)

Drawbacks and risks

A positive result without symptoms usually leads to antibiotic treatment of an infection that might have cleared up on its own; unnecessary antibiotic use contributes to resistance.
A negative urine result can wrongly reassure you if there was also a risk in the anus or if the test was done within 2 weeks after the contact.

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