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Purpose: The purpose of this study is to identify and compare the factors associated with human papillomavirus(HPV) vaccination intention between male and female high school students. The focus is on the knowledge,attitudes and health beliefs related to HPV. Methods: The participants were 246 male and 298 female studentsfrom an academic high school located in Seoul. Data were collected in June 2017, which were analyzed usingdescriptive statistics, the chi-test, t test, Mann-Whitney U test, Pearson correlation coefficients and logisticregression with SPSS for Windows 21.0. Results: 47.6% of the male participants and 86.2% of the female participantsindicated HPV vaccination intention. The median score of the HPV knowledge level was 0 (total score:16)in the boys and 3 in the girls (p<.001). There were significant differences in attitudes and health beliefs relatedto HPV by gender. Religion (OR=0.50), sexual experience (OR=0.09), safety concerns (OR=0.65), perceivedneeds (OR=1.59), importance of prevention (OR=1.78) and perceived susceptibility (OR=1.80) determined HPVvaccination intention in the male students, whereas awareness of HVP vaccination (OR=2.25) and importanceof prevention (OR=1.92) significantly predicted HPV vaccination intention in the female students. Conclusion: Theresults of this study suggest that different strategies need to be taken for different genders: education focusingon safety concerns as well as perceived needs, importance of prevention and perceived susceptibility for malestudents and education emphasizing importance of prevention for female students.