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Be pro-active. Assess. Test. Treat.

Cervical Swab or Urine Test?

Which is best when screening young women for Chlamydia: cervical swab or urine test?

A cervical swab provides the most sensitive and specific test result for Chlamydia, and has the added advan­tage of the physician being able to assess the patient’s general genital health. Screening is easily done during routine Pap tests and is still considered best practice by the Simcoe Muskoka District Health Unit.

What do young women prefer?

Research shows fear or discomfort with pelvic exams is a barrier to youth seek­ing screening for Sexually Transmitted Infections (STI). Almost all studies show that women prefer self-collection of urine samples to a pelvic exam.1 Health Canada’s STI Guidelines now recommend “increased acceptance of testing by using a non-invasive urine-based nucleic acid amplification test (NAAT).”2

How do cervical swab and urine test compare for accuracy?




Cervical Swab NAAT



Urine NAAT



Urethral Swab NAAT



Urine NAAT



NAAT: Nucleic acid amplification test

*Sensitivity: Ability to test to correctly identify cases with disease (true-positives)

†Specificity: Ability to test to correctly identify cases without disease (true-negatives)


 What does the Simcoe Muskoka District Health Unit recommend?

Cervical swab for females when: Use urine based NAAT testing for females when: 
Symptomatic for a STI, or Not due for a Pap test, or
Due for a Pap test, or The patient refuses a pelvic exam, or

Had sexual contact with a person infected with Chlamydia

Patient is menstruating (blood and mucus interfere with swab NAAT testing performance and can result in false-negative results)


Tips for collecting the most accurate urine samples from females4

  • The patient should not urinate for at least one hour prior to collecting the specimen.
  • Collect the first 15 – 20 ml of void­ed urine (not midstream) to a maxi­mum of 60 ml.
  • Ensure the lid is secure; the lab will reject leaking specimens.
  • Store and transport to the test site at 2 – 8 degrees Celsius within 4 – 6 days of collection; do not freeze.
  • Submit specimen as Chlamydia only, Gonorrhea only, or duplex test for Chlamydia and Gonorrhea.
  • Duplex testing requires one specimen and one data sheet.

Collection Kits

Get collection kits from your local Public Health Laboratory. Consult private laboratories for their specific test information and guidelines.


Best Practice

Follow the Public Health Agency of Canada’s 2008 STI Guidelines and screen all sexually active women under age 25. Test for Chlamydia and Gonorrhea during routine Pap tests. The urine based nucleic acid amplification test (NAAT) can be used for asymptomatic female patients who are not due for a Pap test but have a risk factor. Tell your patients if their test is positive, a public health nurse will be calling for follow up.


Simcoe Muskoka District Health Unit

Free fact sheets, free STI medications for patients and partner(s) who test positive for Chlamydia, call the Sexual Health Program, 721-7520 (or toll free 1 877 721-7520)


For additional information and references, visit SMDHU Sexual Health

AIDS & Sexual Health InfoLine, 416-392-2437


Other Resources

Free urine and swab test kits, call Laboratory Services, Ministry of Health and Long-Term Care, 705-329-6001

Canadian Guidelines on Sexually Transmitted Infections (2008)



1. Koku, E. F., (2006). Barriers, Strategies to Promote STI testing among Youth (15–24 yrs): A Literature Review. Toronto Public Health, 6.

2. Canadian Guidelines on Sexually Transmitted Infections (2008)

3. Chlamydia trachomatis and Neisseria gonorrhoeae - Sensitivity and Specificity Comparison of BD DNA Assay to Culture (February 2007) Public Health Laboratories Ontario

4. Specimen Collection Guide (March 2009) Public Health Laboratories Ontario Agency for Health Protection and Promotion

Adapted with permission from Toronto Public Health





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