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Urine or swab: which STI sample you need

Chlamydia and gonorrhoea only show up in a sample from the part of the body they’ve infected. A urine sample checks the penis, a vaginal swab checks the vagina, and throat and anal swabs check those sites. Here’s which samples the Australian STI Management Guidelines recommend for the sex you have, and why one urine sample often isn’t enough.

Key facts

Penis
First-pass urine
Vagina
Self-collected vaginal swab (preferred), or first-pass urine
Anal sex (receptive)
Anal swab
Oral sex
Throat swab, if recommended for you
HIV
Blood: a fingerprick self-test or a lab blood test
Syphilis and hepatitis
Blood from a vein, at a clinic or pathology centre

Why the sample has to match the site

Chlamydia and gonorrhoea can infect the urethra, the vagina and cervix, the anus and the throat. The lab test, a nucleic acid amplification test (NAAT, usually PCR), looks for the bacteria’s genetic material in the sample it’s given. It’s highly sensitive, but it can only find an infection that’s in that sample.

So a urine test only tells you about the urethra. It says nothing about your throat or anus. That matters because those infections are the quiet ones: the guidelines note that anal and throat gonorrhoea cause no symptoms in most people, so they’re only found when those sites are tested.

Which sample, by the sex you have

These follow the Australian STI Management Guidelines (opens in new tab). If more than one row fits you, you need each of those samples.

If you’ve hadSample the lab needs
Any sex using your penis (vaginal, anal or oral)First-pass urine
Vaginal sex, or oral sex on your vaginaVaginal swab, or first-pass urine if you’d rather
Receptive anal sexAnal swab
Oral sex on a partner, if you’re a man who has sex with men or have more than one partnerThroat swab

Men who have sex with men are tested at all three sites – throat, anus and urine – whatever sex they’ve had recently, as the guidelines recommend. Trans and gender diverse people follow the same advice, based on the anatomy you have now and the sex you have. For more on throat testing, see oral sex and STIs.

Vaginal swab or urine?

Both work, but the guidelines say a self-collected vaginal swab is the best sample when you’re not being examined, and that urine is less sensitive than a vaginal swab for chlamydia and gonorrhoea. If a swab doesn’t suit you, a urine sample is a reasonable alternative. When you request testing with Prickly, you can choose either.

What “first-pass urine” means

It’s the first part of the stream, not a midstream sample. The bacteria collect in the urethra, and the first few millilitres wash them out. For the best sample:

  • Wait at least an hour after you last peed.
  • Catch the first part of the stream, about 20 ml, then finish peeing into the toilet.

Collecting your own swabs

Self-collection isn’t second best. The guidelines say people without symptoms can collect most samples themselves, including vaginal, anal and throat swabs, and many clinics hand you the swab and a private room to do exactly that. Each swab takes about 10 seconds, and the self-collection guide shows every step.

Blood tests are separate

HIV, syphilis and hepatitis are found in blood, not in urine or swabs. The guidelines recommend HIV and syphilis testing whenever STI testing is done.

  • HIV: a fingerprick self-test you read at home, or a lab blood test, which picks up HIV sooner after an exposure. See HIV testing at home.
  • Syphilis and hepatitis: blood drawn from a vein. Prickly doesn’t test for these, so ask a sexual health clinic (opens in new tab) or GP clinic (opens in new tab) to include them.

How at-home testing works with Prickly

Prickly is an Australian at-home STI testing service for people without symptoms. When you request testing, you tell us which parts of your body you’ve used for sex, and a doctor confirms which samples suit you before anything is sent.

  • Request online. Complete a five-minute online request, or book a short call with a doctor – bulk billed with Medicare. Either way, a doctor confirms that at-home STI testing is suitable for you.
  • Receive your equipment. Collection equipment tailored to your exposures ships the same or next business day in an unmarked mailer box with Australia Post tracking.
  • Collect at home. Follow the included STI testing self-collection guide – swabs and urine for the lab, and, if you’ve added HIV testing, a fingerprick HIV self-test you read at home in 15 minutes.
  • Post to the lab. Post your lab samples back the same day using the included prepaid return label – at any Australia Post Office, red street posting box or Parcel Locker.
  • Get your results. A doctor reviews every lab test result and emails you privately. Telehealth follow-up included – with help accessing treatment and telling partners, if needed.

The same steps are on the home page under How it works, and fees are under Pricing.

When at-home testing isn’t right

See someone in person at a sexual health clinic (opens in new tab), GP clinic (opens in new tab) or urgent care clinic (opens in new tab) instead if you have symptoms or if you’re under 16. And if you may have been exposed to HIV in the last 72 hours, don’t wait for a test – visit www.getpep.info (opens in new tab) or go to a sexual health clinic (opens in new tab) or emergency department (opens in new tab) as soon as you can. If something happened without your consent, 1800RESPECT (opens in new tab) is also available 24/7 for free, confidential support.

Dr Tom Morley
BMedSc, MBBS, MIPH, FRACGP
Prickly medical director

Medically reviewed on 5 November 2026. This page is general information, not medical advice, and it doesn’t replace a consultation with a doctor who knows your history.

Sources

  1. Australian STI Management Guidelines for use in primary care – Standard asymptomatic check-up (opens in new tab), ASHM.
  2. Australian STI Management Guidelines – Chlamydia (opens in new tab), ASHM.
  3. Australian STI Management Guidelines – Gonorrhoea (opens in new tab), ASHM.
  4. Australian STI Management Guidelines – Men who have sex with men (opens in new tab), ASHM.