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Human papilloma virus (HPV) is a DNA virus associated with the development of cervical, penile, anal, vulvar, and oral cancers. In recent years, there has been an increase in oral cancer, which could be due to changes in sexual behavior in the general population. In México, there is scarce information on this regard, which prompted us to study HPV infection prevalence in the oral cavity of an indigenous community from the municipality of Siltepec, Chiapas, Mexico. Oral samples from 198 individuals were obtained with cytobrush for virus detection by nested PCR, using MY09/MY11 and GP5+/GP6+ primers, and positive samples were sequenced for HPV genotyping. We observed 12.1% HPV infection prevalence, which depended on gender, number of sexual partners, lack of using condoms, and oral sex practices. In contrast, no significant association between HPV infection and tobacco or alcohol consumption was detected. Furthermore, sequencing analyzes were performed where HPV-13 (21/24), -16 (2/24), -32 (1/24), -81 (1/24), and -83 (1/24) were evidenced and HPV-16 European/Asian and Asian/American E6 variants identified. These results demonstrated an important prevalence of HPV infection in the oral cavity of a Mexican indigenous community, where the predominant genotypes were associated with benign pathologies, and showed that high-risk genotype variants derived from different lineages. Unlabelled Image • Prevalence of HPV infection in the oral cavity of a Mexican indigenous community • Predominant genotypes were associated with benign pathologies. • High-risk genotype variants derived from different lineages. [ABSTRACT FROM AUTHOR]