The aim of this work was to determine human papilloma virus (HPV) high and low risk (HR and LR) genotypes prevalence, and other HPV infection associated risk factors, in men who have sex with men (MSM). A cross-sectional study was conducted, to this end, 104 MSM responded a social demographic and sexual behavior questionnaire and consented sampling of anal epithelium for molecular analysis by polymerase chain reaction (PCR), with β-globin primers as internal control, and HPV L1 region primers. Subsequently, typing was performed by sequencing. Prevalence of HPV in MSM was 34%: 10% HR and 24% LR. The most frequent oncogenic HPV types were 16 (20%), 73 (20%) and 45 (20%), and non-oncogenic VPH 11 (36%), 62 (28%) and 6 (12%). MSM less than 30 years old had greater HPV prevalence. Presence of human immunodeficiency virus (HIV) was not significantly associated to HPV infection in the studied population.