Human papillomavirus (HPV) detection and typing using the PapilloCheck test and cytological examination were carried out in anal samples collected from 67 men seropositive for human immunodeficiency virus (HIV) who have sex with men. Fifty (74.6%) patients had anal HPV infection, 46 (68.7%) had high-risk (HR) HPV infection, and 38 (56.7%) had multiple infection involving 2-9 (median, 3) HPV types. The HPV types identified most frequently were HPV 44/55 (19.4%), HPV 53 (19.4%), HPV 16 (16.4%), HPV 39 (16.4%), and HPV 42 (14.9%). Thirty-two of the 66 interpretable smears (48.5%) revealed cytological abnormalities: 9 (13.4%) atypical cells of undetermined significance, 20 (30.3%) low-grade intraepithelial lesions, and 3 (4.5%) high-grade intraepithelial lesions. Cytological abnormalities were associated significantly with HPV detection (P < 0.001), multiple HPV infection (P < 0.001), and increased number of HPV types (P < 0.001). The HPV types associated most frequently with cytological abnormalities were HPV 39 (28.1%), HPV 42 (28.1%), HPV 53 (28.1%), HPV 16 (25.0%), HPV 44/55 (25.0%), and HPV 59 (21.9%). HPV DNA detection as well as cytological abnormalities were associated neither with HIV RNA detection in plasma nor with CD4+ T-cell count. Differences in age or in time since HIV acquisition were not observed in patients with or without cytological abnormalities. The present study confirms the high prevalence of anal HR-HPV infection and cytological abnormalities in men infected with HIV who have sex with men. HPV testing and/or cytological analysis may be helpful in selecting the patients to be referred to proctological examination.