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Human papillomavirus (HPV) infection is associated with cancer and can be prevented through vaccination. Few studies from Taiwan have reported on HPV infection among human immunodeficiency virus (HIV)-infected subjects. The aim of this study was to examine the prevalence of HPV infection among men who have sex with men (MSM) with and without HIV infection in Taiwan, and explore the behavioral risk factors thereof.We conducted a cross-sectional study in Taiwan during 2013 to 2016 to collect data on MSM aged 20 years or older. We used a questionnaire in a face-to-face interview, and subsequently collected oral, anal, and genital specimens from HIV-infected and HIV-uninfected subjects. Multivariate analysis was performed to predict factors associated with high-risk HPV (HR-HPV) positivity.Overall, 279 subjects, including 166 (59.5%) HIV-uninfected and 113 (40.5%) HIV-infected men were enrolled. Compared to HPV-negative subjects, HPV-positive subjects had significantly higher rates of receptive anal sex (91.3% vs 75.6%), substance use (22.6% vs 11%), history of sexually transmitted infections (75.7% vs 38.4%), anogenital or oral warts (39.1% vs 6.72%), syphilis (32.2% vs 11.6%), and HIV infection (69.6% vs 20.1%). We detected 489 HPV deoxyribonucleic acid (DNA) types (through 379 viable specimens), of which 43.6%, 5.7%, 56.4%, and 10.4% were HR-HPV type, HPV type 16, low-risk HPV types, and HPV type 6, respectively. In multivariate analysis, HIV-infected subjects had a significantly higher prevalence of HR-HPV infection (adjusted odds ratio, 5.80; 95% confidence interval, 2.57–13.11), compared to HIV-uninfected subjects.These results suggest that the prevalence of HPV infection was high among HIV-infected MSM. Additionally, anal HPV infection was observed to be common among both HIV-infected and HIV-uninfected MSM in Taiwan. The prevalence of oral and genital HPV infection, HR-HPV DNA types, and multiple HPV types was higher in HIV-infected subjects than in HIV-uninfected subjects. As only 35% of subjects practiced safe sex, we recommend routine HPV vaccination with 4-valent HPV or 9-valent HPV vaccines for both MSM, and HIV-infected subjects.