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BACKGROUND: Oral human papillomavirus (HPV) prevalence varies according to geographical occurrence, the type of lesion, and the method of diagnosis. The polymerase chain reaction method (PCR) appears to be more sensitive and can be easily applicable to epidemiologic studies. OBJECTIVES: To determine the frequency of HPV and its genotypes in oral lesions among patients attending a reference clinic of a university hospital. METHODS: PCR was performed to identify HPV DNA from samples of oral epithelial lesions in 80 patients. For HPV DNA amplification, MY09/MY11 consensus primers were used and specific genotypes were identified through restriction fragment of length polymorphism (RFLP) pattern. RESULTS: HPV DNA was present in 11.3% of patients, and the identified genotypes were 6b, MM4 (W13B), and MM9 (PAP238A). CONCLUSIONS: HPV DNA frequency in patients with oral epithelial lesions was 11.3%. The genotypes MM4 and MM9 are uncommon in oral lesions, and they are characterized as high-risk HPV types in those types of lesions. [ABSTRACT FROM AUTHOR]