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Efficacy, immunogenicity and tolerability of the human papillomavirus (HPV)-16/18 AS04-adjuvanted vaccine were evaluated in Japanese women aged 20–25 years, for which results have been reported previously. We analyzed the baseline data from that study and report the prevalence rates of HPV infection in young healthy Japanese women. One thousand and the forty Japanese women aged 20–25 years were enrolled in a phase II, double-blind, controlled, randomized, multicenter study. At study entry, cervical specimens were collected from the women and tested by line probe assay for 25 HPV-types and by HPV-16/18-specific polymerase chain reaction. The most frequently detected HPV-type in baseline cervical specimens was HPV-52 (8.1%), followed by HPV-16 (6.5%), HPV-51 (4.5%), HPV-18 (4.0%) and HPV-31 (3.8%). The proportion of HPV DNA-positive women increased with severity of cytological abnormalities: 26.1% (237/908) in normal cytology, 93.3% (70/75) in low-grade squamous intraepithelial lesion and 100% (7/7) in high-grade squamous intraepithelial lesion. The relative contribution of HPV-16 and HPV-18 was 4.1 and 3.0% for normal cytology cases, and 20.0 and 16.0% in low-grade squamous intraepithelial lesion, respectively. HPV-16 was found in four of seven high-grade squamous intraepithelial lesion cases (57.1%) and five of the six cervical intraepithelial neoplasia 2+ cases (83.3%). Multiple and single HPV infections were observed in 13.5% (140/1039) and 20.7% (215/1039) of all women, respectively. The HPV prevalence rates in Japanese women aged 20–25 years underline the importance of HPV vaccination at a young age and this report should be useful for monitoring changes in HPV prevalence after widespread HPV vaccination in Japanese women. (Cancer Sci 2011; 102: 877–882)