Objectives: The purpose of this study was to find out the suicide ideation of high school students in urban and rural areas, and especially to research the relationship between suicide ideation, and general characteristics, characteristics of school life, and empirical characteristics of suicide. Methods: This research targeted four urban and four rural high schools in two cities. The study subjects were 1,114 students in urban area and 968 students in rural area, total 2,082 students. The survey was conducted from July 1, 2009 to July 31, 2009. For statistical analysis, chi-square test, t-test and ANOVA were used for investigating related factors with suicide ideation in urban and rural areas, respectively, with multiple logistic regression for multivariate analysis. Results: The results showed that 38.8% of respondents had suicide ideation within 1 year. The percentage of female students (44.8%) was significantly higher than that of male students (33.4%). However, there was no significant difference between urban (38.0%) and rural area (39.9%). The significant influencing factors on suicide ideation in multiple logistic regression were gender [female student OR(odds ratio)=1.80 (95% CI 1.31-2.47) compared with male student] and grade [second year OR=1.40 (95% CI 0.98-2.00), third year OR=2.15 (95% CI 1.49-3.12) compared with first year] in urban area. Those in rural area were gender [female student OR(odds ratio)=2.71 (95% CI 1.23-2.38) compared with male student], economic deterioration [yes OR=1.81 (95% CI 1.24-2.64) compared with no], and grade [second year OR=2.80 (95% CI 1.82-4.32), third year OR=3.84 (95% CI 2.52-5.87) compared with first year]. Conclusions: This study showed about 40% of high school students had suicide ideation within 1 year. A suicide prevention program may be implemented considering factors related with suicide ideation identified in this study.