Objectives The relationship between sexual practices, identity and role among Latino men who have sex with men (MSM) and HIV risk is the subject of ongoing investigation but less is known about how these aspects of sexuality relate to human papilloma-virus (HPV), an independent risk factor for HIV. This observational study investigated the relationship between HPV and sexual practices, identity and role as well as other sexually transmitted infection (STI)/HIV risk factors among HIV-negative heterosexually and homosexually identified Peruvian MSM. Setting Community-based clinic for MSM in Lima, Peru. Participants 756 subjects were screened based on inclusion criteria of: Born anatomically male; age ≥18 years; had any anal intercourse with a man during the previous 12 months; residing in metropolitan Lima; HIV negative; willing to commit to twice-yearly clinic visits for 24 months; had not participated in an HIV or HPV vaccine study. 600/756 participants met the inclusion criteria and were enrolled, of whom 48% (284) identified as homosexual and 10% (57) as heterosexual, the basis of the analyses performed. Results Compared with homosexually identified MSM, heterosexually identified MSM had completed fewer years of formal education and were less likely to have: Anogenital HPV or visible anal warts; given oral sex to a man; or used a condom with their most recent female sexual partner (all p<0.05). Conversely, heterosexually identified MSM were more likely to have: Visible penile warts; used a condom during last anal intercourse; smoked cigarettes; had transactional sex; and used drugs during sex in the previous month (all p<0.01). There was no difference found between heterosexually and homosexually identified MSM by syphilis or high-risk HPV prevalence. Conclusions HPV burden, wart type (penile vs anal) and select HIV/STI risk behaviours differed between heterosexually and homosexually identified Peruvian MSM. Understanding the implications of these differences can lead to tailored HIV/STI prevention interventions for heterosexually identified MSM.