Using nucleotide sequencing-based genotyping, we conducted a case-control study to examine cervical cancer risk associated with human papillomavirus (HPV) infection in a Japanese population. A consensus primer pair was used to amplify DNA from the L1 region of HPV by polymerase chain reaction (PCR). By PCR, 311 of 356 patients with cervical cancer and 333 of 3249 control individuals were positive for HPV. By the direct sequencing of PCR products, nucleotide sequences of 30 genotypes were obtained. A high incidence of type 52 and a low incidence of type 16 were characteristic of the control group. Odds ratios were estimated for 18 genotypes. Types 71, 90, and 91, previously uncharacterized, were classified as low-risk genotypes, which is consistent with predictions made on the basis of phylogeny. The present study is the first large case-control study of its kind to use nucleotide sequencing-based genotyping.