Objective We analyzed subtypes of human papilloma virus (HPV) infection in Papanicolaou (Pap) smear results of women in Jeju island, Korea. Methods We investigated the distribution of HPV subtypes according to Pap smear results among 635 women in Jeju island, Korea between October 2005 and October 2010. Results The most prevalent HPV subtypes were HPV 16, 52, 53, 58 in negative Pap smear result and HPV 16, 52, 31, 53, 66 in atypical squamous cell, HPV 52, 53, 56, 66 in low grade squamous intraepithelial lesion, HPV 16, 58, 52, 33, 33 in high grade squamous intraepithelial lesion/squamous cell carcinoma each other. The subtypes of HPV 16, 52, 53, 58, 31 were common in all women participated in study from Jeju island, Korea. And multiple infections were more common in women under 30 years of age than above age as previous study and the majority of HPV multiple infections were high risk types (94.5%). Conclusion This prevalence was some different from previous study of Korean other region, but more similar to Japanese study data. We think this result shows that Jeju island women maybe have the genetic, regional or environmental close relationship with Japanese because of close distance and culture irrespective of different national race.