Human papillomaviruses (HPVs) have been recognized as etiologic factors in cervical carcinoma andseveral other anogenital cancers in females and males. HPV are classified as low risk (LR), probable high riskand high risk (HR) on the basis of their oncogenic potential. HPV genotypes, which are crucial for diagnosisand relationship with carcinogenesis, have been determined by several genotyping methods. In this study, twogenotyping methods were compared: direct sequencing and INNO-LiPA. In total, 2,494 cervical specimens weretested and 27.2 % of these were found to be HPV DNA positive with 24.5% showing normal cytology. Specimenswere divided into four groups according to their pathological cytology as normal, LSIL, HSIL and cancer and 134specimens were selected for HPV genotyping by both methods. HPV genotyping results showed 87.5% positivecorrelation. With 17 specimens, the results were discordant, 12 specimens showed different genotypes. Othershad genotypes that could not be typed by the INNO-LiPA method. Neither did direct sequencing in 3 differentregions yield unequivocal results. Both genotyping methods have advantages and disadvantages. Consequently,the method most suitable for the study objective, budget and predominance of HPV genotype in any given areashould be selected.