Objective To detect the most prevalent human papillomavirus (HPV) genotypes in cervical smear samples of asymptomatic Peruvian women by analyzing the correlation between Papanicolaou (PAP)-stained cervical tests and PCR-sequencing. Methods A total of 254 women attending routine gynecological examinations were included in this study. The samples were analyzed by PAP technique and examined under a microscope by a pathologist and classified by the Bethesda system. HPV amplification was done using the primers specific for E1 region and positive specimens were confirmed by direct sequencing. Results The prevalence of HPV was investigated in 254 cervical scrape samples by PCR. PAP smear showed that 94.9% cases had normal morphology and 5.1% had an inflammatory pattern; 20.5% were found to be infected with HPV, comprising 20 different genotypes. HPV16 was the most prevalent genotype in correlation with changes in cervical cytology. Conclusions Our results suggest the HPV is very frequent even in women with negative PAP, and PCR seems to be the best option to determine the causative agent of HPV infection in endocervical samples. Identification of the HPV genotype in asymptomatic women may allow the implementation of appropriate prophylactic measures which may have a direct impact on the natural history of the disease and the subsequent development of cervical malignancy.