Background: The importance of school contextual effects on health and well-being among young people is currently recognized. This study examines the contextual effects of school satisfaction as well as the effects of individual-level school satisfaction on health-risk behaviors in Japanese high school students. Methods: Self-administered questionnaires were distributed to 3248 students in grades 10 through 12 at 29 public high schools throughout Okinawa, Japan. Using multilevel logistic regression models, the effects of individual- and contextual-level school satisfactions on health-risk behaviors were analyzed. The contextual-level school satisfaction was defined as satisfaction at the school level and was measured using aggregated individual scores. Behaviors studied included current smoking, current drinking, and sexual activity. Results: Approximately 15%, 6%, and 5% of the total individual differences in smoking, drinking, and sexual behaviors, respectively, occurred at the school level. Students with lower school satisfaction were more likely to engage in health-risk behaviors compared with those with higher school satisfaction. After adjustment for individual-level school satisfaction and other covariates, the odds of smoking and drinking increased with decreasing contextual-level school satisfaction. However, the association of contextual school satisfaction with sexual activity did not reach statistical significance. Conclusions: This study showed that individual- and contextual-level school satisfactions affected smoking and drinking behaviors in Japanese high school students. However, no significant association between contextual-level school satisfaction and sexual activity was observed. (Contains 3 tables.)