Human papillomaviruses (HPVs) have been recognized as etiologic factors in cervical carcinoma and several other anogenital cancers in females and males. HPV are classified as low risk (LR), probable high risk and high risk (HR) on the basis of their oncogenic potential. HPV genotypes, which are crucial for diagnosis and relationship with carcinogenesis, have been determined by several genotyping methods. In this study, two genotyping methods were compared: direct sequencing and INNO-LiPA. In total, 2,494 cervical specimens were tested and 27.2 % of these were found to be HPV DNA positive with 24.5% showing normal cytology. Specimens were divided into four groups according to their pathological cytology as normal, LSIL, HSIL and cancer and 134 specimens were selected for HPV genotyping by both methods. HPV genotyping results showed 87.5% positive correlation. With 17 specimens, the results were discordant, 12 specimens showed different genotypes. Others had genotypes that could not be typed by the INNO-LiPA method. Neither did direct sequencing in 3 different regions 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 area should be selected.