Background: The incidence of anal cancer has increased in developed countries. There is evidence that high-grade anal intraepithelial neoplasia and anal cancer are both linked to some human papillomavirus (HPV) infections. There are scarce data on anal cancer or male anal HPV infection in Brazil. Objective: The purpose of this study was to assess the prevalence of anal HPV infection and associated risk factors, stratified by oncogenic and nononcogenic types, in a sample of HIV-seropositive men in Brazil. Methods: Multicenter cross-sectional study of HIV-seropositive male patients attending public AIDS clinics in urban Brazil. Participants were interviewed for sociodemographic and behavioral characteristics. Anal HPV specimens were collected with a moistened Dacron swab inserted into the anal and stored in ThinPrep solution. HPV DNA–positive samples were typed by dot-blot hybridization. The prevalences of oncogenic and nononcogenic HPV types were calculated and multinomial logistic regression was used to assess independent predictors of HPV infection. Results: Among 445 men, 65.6% were positive for HPV DNA in the anal canal. Oncogenic types were detected in 40.7%. Logistic regression indicated that lifetime history of sexual intercourse only with men or with men and women; receptive anal intercourse in the last 12 months; and CD4+ lymphocyte count below 200 cells per cubic millimeter were independently associated with the detection of anal HPV infection. Conclusions: The high prevalence of anal HPV infection in this cross-sectional study underscores the need for studying and implementing screening programs of high-risk groups in Brazil.