Oncogenic human papillomavirus (HPV) infection is a cause of many anogenital cancers in women and men; however, there is little research on HPV prevalence and risk factors that includes both women and men from the same population. A total of 4687 participants, including 2378 women and 2309 men aged 18-55 years old from the same community, were enrolled in the study in Liuzhou, China. Exfoliated cells were collected from the participants from different anatomic sites and were tested for 13 oncogenic and 3 non-oncogenic HPV types. The prevalence of any oncogenic HPV type was higher in women than in men (18.7% vs 9.4%, P<0.001), whereas the prevalence of HPV 6 and 11 infection was similar (1.4% vs 1.2%, P=0.6832). HPV 52, 58, 16, 39 and 18 were the five most prevalent types in both sexes. Sexual and hygienic behaviors were associated with HPV infection in both women and men. We found that oncogenic HPV DNA detection is more prevalent in women than in men in China, whereas the prevalence of HPV 6 and 11 is similar in both sexes. The data indicate that the interaction of host and virus might be different among high- and low-risk HPV types.