The main aim of this article is to assess the relationship between the structural and (health) policy variables of the school and characteristics of the individual on the risk and health behaviour of adolescents. Individual and school level effects on seven health-related behaviours are simultaneously estimated, using multilevel modelling. The data are from the Flemish health behaviour in school-aged children study in Belgium. Data are used from 29 Flemish schools in which students (N=3225), school administrators (N=29) and teachers (N=1132) were surveyed with anonymous written questions. The analysis confirms previous findings concerning individual level effects. Although differences between schools in risk and health behaviour were found to originate mainly from differences in pupil characteristics, substantial variation between schools remained with regard to regular smoking, drinking habits and tooth brushing after controlling for individual effects. A wide range of school structure and policy variables were taken into account, but only few of them were found to influence the health and risk behaviour of young people. Moreover, the study could not detect an effect of health promotion policy at school. The analysis therefore only partially confirms the hypothesis that the school has an impact on the health behaviour of young people. The findings demonstrate the need for a more thorough examination of the paths by which schools can influence the health behaviour of their pupils.