AIM: Human papillomavirus (HPV) in the oral cavity has been retrospectively associated with an increased risk of developing HPV-positive head and neck squamous cell carcinoma (HNSCC). The aim of this study was to determine the prevalence of oral HPV infection in a local population of New Zealand women aged 18 to 25 years, including determination of HPV genotypes, and to assess potential risk factors for oral HPV infection using participant questionnaire responses. METHODS: Oral brushings and questionnaire responses were collected from 234 women recruited from sexual health and student health centres. Questions covered age, ethnicity, sexual partners, alcohol consumption and smoking. PGMY primers were used for HPV detection by PCR, and results confirmed by sequencing and the cobas® 4800 HPV system. RESULTS: The prevalence of HPV infection was 3.2% of 216 women (95% CI: 1.6%-6.5%). Samples from two women (0.9%, 95% CI: 0.3%-3.3%) contained oncogenic HPV, and another five (2.3%, 95% CI: 1.0%-5.3%) were positive for HPV 13. No significant associations were found between putative risk factors and the presence of oral HPV infection. CONCLUSION: The prevalence of HPV in the oral cavity of New Zealand woman was comparable to results of other studies, but showed an unusual distribution of HPV types. The comparatively high detection rate of HPV 13 suggests that further work into clinical significance of oral HPV 13 infection is warranted.