Background: HPV infection is the most common sexually transmitted viral infection, and is associated with several neoplasms. Aim: To describe the epidemiology, natural history and risk factors associated with oral HPV infection in asymptomatic young adults. Methods: A prospective and longitudinal study was conducted, including subjects without oral pathology, who were sampled from the oral mucosa. All subjects with positive results were re-sampled 6 months later. The presence of HPV was identified by PCR. Demographic and sexual behavior data were obtained with a survey that was responded without the intervention of the researcher. Results: 102 samples were collected from subject of 18-26 years old, 60 (58.8%) were male. The prevalence of the virus was 6.9%; all positive subjects had active sexual life. Same-gender relationships were the only variable associated with the presence of the virus (p < 0.05). At six months all subjects had eliminated the virus. Conclusion: Oral HPV infection is transient and is associated to same-gender relationships, mainly women who have sex with women.