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Background Human papillomavirus (HPV) is associated to the pathogenesis of various cancers, such as oropharyngeal squamous cell carcinoma, which has a high incidence in Puerto Rican men. Despite the burden of oral cancer in Puerto Rico, little is known about the epidemiology of oral HPV infection, particularly in high-risk men. Therefore, this study is aimed at determining the prevalence of oral HPV infection, the genotype distribution and correlates associated with oral HPV infection in men of at least 16 years of age attending a sexually transmitted infection (STI) clinic in Puerto Rico. Methods A cross-sectional study consisting of 205 men was conducted. Participants provided a 30-second oral rinse and gargle with mouthwash. Following DNA extraction, HPV genotyping was performed in all samples using Innogenetics Line Price Assay (INNO-LiPA). A questionnaire was administered, which included a demographic, behavioral and a clinical assessment. Descriptive statistics and bivariate analysis were used to characterize the study sample. Variables that achieved statistical significance in the bivariate analysis (p < 0.05) were assessed in multivariate logistic regression models. Results The mean age of the study sample was 38.5 ± 14.2 years. Oral HPV prevalence among men was 20.0% (95.0%CI = 14.8%-26.1%) and of HPV type 16 was 2.4% (95.0%CI = 0.8%5.6%). Oral HPV prevalence significantly increased over increasing age categories (p-trend = 0.001). Multivariate analysis showed that oral HPV was independently associated with number of sexual partners (adjusted OR = 1.02; 95%CI = 1.01-1.03) and lifetime use of cigarettes (adjusted OR = 3.00; 95%CI = 0.98-9.16). Conclusions Oral HPV among the sampled men in the STI clinic was high, regardless of the HIV status or sexual behavior. Interventions in STI clinics should include screening for HPV in the oral cavity for the early detection and reduction of long-term consequences of oral HPV infection, such as oropharyngeal cancer. [ABSTRACT FROM AUTHOR]