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First-Void Urine: Why the First Part of the Stream Matters for Detecting Pathogens

Whether you want to know why it burns when you urinate, you're dealing with ongoing pelvic pain, or you want to check for a urinary tract infection, HPV, herpes or another infection, the sample matters as much as the test. First-void urine (also called first-catch urine) is the very first part of the urine stream, roughly the first 20 mL, collected without stopping to clean or discard anything first. It is not the same as the "midstream clean-catch" sample most people are used to giving at a doctor's office.

Why the first part of the stream carries more

Many infections that cause urinary symptoms live in the urethra and the genital tract, not only in the bladder. When you start to urinate, the first rush of urine flushes the urethra and picks up mucus, cells and organisms on the way out, while still containing urine from the bladder. In women, it also carries secretions from the vagina and cervix. Researchers have shown that the first collected part of a urine void contains more HPV DNA than the parts that follow.1

A midstream sample is designed for the opposite purpose: it deliberately lets that first portion go, so that what is collected reflects only the bladder. That approach was built for traditional bladder cultures, but it washes away much of what can explain symptoms that start in the urethra.

"Why does it hurt when I pee?"

Burning or pain with urination is not always a bladder infection. It is also the most common symptom of urethritis, inflammation of the urethra, reported by more than half of patients.2 Organisms linked to urethritis include Chlamydia trachomatis, Mycoplasma genitalium, Ureaplasma urealyticum and Trichomonas vaginalis, and molecular testing of first-void urine is the recommended approach for anyone with suspected urethritis.2

Herpes can cause it too. Herpes simplex virus (HSV) is a recognized cause of urethritis, and it can bring severe burning with urination.10 Researchers have detected both HSV-1 and HSV-2 by PCR in first-stream urine from men with urethritis.11 In our own lab, first-void urine testing has identified HSV-2 in patients whose symptoms presented as urethritis.

Several of these organisms do not grow on a routine urine culture, which is one reason a standard test can come back "negative" while the symptoms continue. See how PCR compares with culture.

Ureaplasma: common, and rarely tested

Ureaplasma is one of the most common organisms found in the urogenital tract, and also one of the least often tested. It cannot grow on a routine urine culture, which needs special media for it,12 and standard chlamydia and gonorrhea tests do not look for it. Its role in symptoms is still debated: some studies have linked higher levels of U. urealyticum to urethritis while others have not,13 and it is among the organisms most often detected in men with chronic prostatitis.4 That is why our test tells Ureaplasma urealyticum and Ureaplasma parvum apart and reports how strongly each is detected, giving your healthcare provider more to go on than a simple positive or negative.

Chronic pelvic pain and prostatitis

For men with chronic prostatitis or chronic pelvic pain, the first-void sample has long been part of the standard workup: the classic Meares–Stamey localization test begins with a first-void urine sample to check the urethra before testing the bladder and prostate.3,4 In a 2025 study of chronic prostatitis patients, Ureaplasma urealyticum and Chlamydia trachomatis were the most common sexually transmitted organisms detected, the switch to PCR-based testing increased detection, and the authors note that some cases may involve organisms that cannot be grown in culture at all.4 Finding a treatable infection does not explain every case of pelvic pain, but it is an important question to rule in or out with your healthcare provider.

What the evidence shows for STIs and HPV

  • Chlamydia and gonorrhea. The CDC calls first-catch urine the recommended sample for men, equivalent to a urethral swab. For women it is an accepted screening sample, though the CDC notes a vaginal swab may detect slightly more infections.5
  • Mycoplasma genitalium. Nucleic acid amplification tests for M. genitalium are FDA-cleared for use with urine.6
  • HPV. A 2014 BMJ meta-analysis of 14 studies found urine detected cervical HPV with 87% sensitivity, and that first-void samples were more accurate than random or midstream samples.7
  • Collection device. In a study of HPV-positive women, samples collected with the Colli-Pee® first-void device had higher HPV DNA concentrations than samples collected in a standard urine cup.8

How our kits capture first-void urine

Collecting exactly the first part of the stream into a cup is awkward. Our urine kits use the Colli-Pee® device, which captures the first portion automatically and lets the rest flow into the toilet, with no need to stop and start.9 The collection tube contains a preservative that protects the sample's DNA on its way to our lab.

In the lab, the step that matters most happens before any test is run: releasing and purifying the DNA from the urine. Our sample preparation is a process we developed and validated in-house specifically for urine, and it is one of the main reasons we stand behind our results. Every sample is then tested with PCR-based molecular methods in our own CLIA-certified, high-complexity laboratory in Carlsbad, California.

Tips for a good sample

  • Collect the first urine of the stream. Don't urinate a little into the toilet first, and don't clean the area beforehand.2
  • Follow the timing in your kit's instructions, including how long to wait since you last urinated.
  • Close the tube tightly and mail it promptly with the prepaid return envelope.

See all at-home test kits or read how at-home testing works.

References

  1. Vorsters A, Van Keer S, Van Damme P. The use of urine in the follow-up of HPV vaccine trials. Hum Vaccin Immunother. 2015;11(2):350–352. PMC
  2. Sell J, Nasir M, Courchesne C. Urethritis: rapid evidence review. Am Fam Physician. 2021;103(9):553–558. aafp.org
  3. Meares EM, Stamey TA. Bacteriologic localization patterns in bacterial prostatitis and urethritis. Invest Urol. 1968;5(5):492–518.
  4. Magri V, Perletti G, Stamatiou K. Pathogen detection and diagnostic scenarios in chronic prostatitis. Diagnostics (Basel). 2025;15(6):762. PMC
  5. Papp JR, Schachter J, Gaydos CA, Van Der Pol B. Recommendations for the laboratory-based detection of Chlamydia trachomatis and Neisseria gonorrhoeae, 2014. MMWR Recomm Rep. 2014;63(RR-02):1–19. cdc.gov
  6. Centers for Disease Control and Prevention. Mycoplasma genitalium. Sexually Transmitted Infections Treatment Guidelines, 2021. cdc.gov
  7. Pathak N, Dodds J, Zamora J, Khan K. Accuracy of urinary human papillomavirus testing for presence of cervical HPV: systematic review and meta-analysis. BMJ. 2014;349:g5264. PubMed
  8. Pattyn J, et al. Human papillomavirus detection in urine: effect of a first-void urine collection device and timing of collection. J Virol Methods. 2019;264:23–30. PubMed
  9. Fujirebio. Colli-Pee™ first-void urine collection device, product information. fujirebio.com
  10. Ong JJ, et al. Clinical characteristics of herpes simplex virus urethritis compared with chlamydial urethritis among men. Sex Transm Dis. 2017;44(2):121–125. PubMed
  11. Bradshaw CS, Tabrizi SN, Read TRH, et al. Etiologies of nongonococcal urethritis: bacteria, viruses, and the association with orogenital exposure. J Infect Dis. 2006;193(3):336–345.
  12. Cunningham SA, Mandrekar JN, Rosenblatt JE, Patel R. Rapid PCR detection of Mycoplasma hominis, Ureaplasma urealyticum, and Ureaplasma parvum. Int J Bacteriol. 2013;2013:168742. PMC
  13. Frølund M, Falk L, Ahrens P, Jensen JS. Detection of ureaplasmas and bacterial vaginosis associated bacteria and their association with non-gonococcal urethritis in men. PLoS One. 2019;14(4):e0214425. PMC

This article is for general information and is not medical advice. Talk with a healthcare provider about your symptoms and results.

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