A multi-center study was conducted to examine 6,628 eligible Japanese women aged from 16 to 50 years for uterine cervical abnormality and HPV infection with a liquid based-cytology test and a novel HPV test using the PCR-SSOP-Luminex® method identifying 31 HPV genotypes. In 3,047 normal subjects, the overall prevalence across all HPV types was 25%, while that of the common 13 high-risk (Common-13HR) types (HPV-16, 18. 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, and 68) was 17%, and that of the definite high-risk (Definite-HR) types (HPV-16, 18. 31, 33, 35, 45, 52, and 58) was 12%. For Definite-HR, HPV-52, 16, and 58 were the most common, HPV-31 was relatively common, and HPV-18 was less common, while HPV-33, 35, and 45 were rare. Seven Definite-HR excluding HPV-45 and seven Possible-HR (HPV-39, 51, 56, 66, 68, 70, and 82) HPV types were identified as a single type infection in patients with high-grade squamous intraepithelial lesion (HSIL) or worse. The Common-13HR types were detected in 89% of subjects with HSIL, whereas either Definite-HR or Possible-HR types were detected in 95% of HSIL. These 1420 HPV types appear to be involved with HSIL or worse in Japan. The prevalences of multiple-type HPV infections were identified in roughly half of HPV-positive subjects, and decreased significantly with age in normal population and abnormal cytology groups, although the prevalences of single-type infections increased with age in the latter group. Most HPV infections are cleared for some years, while a certain HR-HPV type persists to induce HSIL. J. Med. Virol. 88:324–335, 2016. © 2015 Wiley Periodicals, Inc.