Objective: This study explored the differences in health behaviors between boys and girls at junior high schools in Yi-Lan county. Study results could be applied to develop gender appropriate programs for health promotion for students in middle school. Method: Stratified random sampling was used and 788 participants were recruited. Data were collected by a structured questionnaire. Result: Boys reported significantly higher levels of physical activity and use of eye protection than girls, but less use of transportation safety, oral hygiene, sun protection. Boys perceived better health status than girls. Conclusion: Study results support the existence of gender differences in various health behaviors of junior high school students. This should be taken into account when planning health promotion and education programs.