HIV facilitates an increase in human papillomavirus (HPV)-associated conditions. HIV-positive men living in a substance use context in Los Angeles, USA, were recruited using respondent-driven sampling, completed a questionnaire and had biological samples including an anal HPV swab taken. A total of 316 evaluable men were enrolled in the study. The prevalence of any HPV, high-risk (HR) infection and multiple-type infection was highest for men who have sex with men (MSM) (93.9%, 64.6% and 29.7%, respectively). When any HPV and HR-HPV prevalence in all men was stratified by age, the youngest group had 100% and 68.2% prevalence, respectively, with similarly high rates maintained up to age 49 years. The individual's use of alcohol, marijuana, cocaine, methamphetamine or heroin was not significantly associated with anal HPV detection. In this marginalized population, high prevalence rates of anal HPV and HR-HPV occurring over a wide age range may increase the individual's risk for anal dysplasia and anal cancer.