A cross-sectional study was conducted to investigate the prevalence, types, and risk factors associated with anal HPV infection among HIV-infected men in outpatient clinics at an AIDS designated hospital in Taiwan. Anal swabs were collect and PCR (polymerase chain reaction) was used to analyze the types of anal HPV infection. HPV DNA was detected in 74.2% of the 198 participants, including high-risk types (40.4%), low-risk types (18.2%) and multiple-types (6%). The most common types were HPV 16 (13.1%), 6 (10.4%), 11 (7.1%) and 18 (6.1%). The significant risk factor for being infected with any type or a high-risk type of HPV was having sexual partners (>3) in the preceding 6 months. Low-risk type of anal HPV infection was associated with a history of anal lesions. Our findings support the need for regular follow-up of all HIV/HPV coinfected patients and their partners to allow early detection of anal intraepithelial neoplasia.