Latin American transgender women are highly vulnerable to HIV infection, and although much is known about factors associated with HIV infection in this population, little is known about the association of human papilloma virus (HPV) with HIV infection. We investigated anogenital HPV and cumulative HIV incidence among 68, initially HIV uninfected, Peruvian transgender women enrolled into a 2-year, prospective cohort study: 95.6% had at least one anogenital HPV genotype at baseline, 19.1% had visible anogenital warts, and 6.0% became infected with HIV over the course of the study. Due to the high anogenital HPV prevalence, this population would likely benefit from early immunization with the HPV vaccine.