The risk behaviours of adolescents, such as alcohol use, gambling and violence, represent a great public health challenge. In order to investigate how inter-school differences in risk behaviours can be explained by a positive school environment, measured via school bonding at the individual and school level, and how risk behaviour differences relate to a negative family environment, a multilevel analysis of individual, family and school factors was conducted. A survey was carried out with a random sample of 20 % of all students from 30 secondary schools in Croatia. The questionnaire used consisted of scales for assessing (1) risk behaviours, (2) socio- demographics, (3) adverse family relations, (4) school bonding and (5) school level variables. Intraclass correlations of 0.094 and 0.101 for risk behaviours and school bonding, respectively, were found. Upon fitting a multilevel model with individual and contextual variables, 94.3 % of the school level variance for risk behaviours was explained. Results indicate that, when the compositional effects of age, gender, family background and student’s own level of school attachment and commitment were held constant, attending a school where students tended to exhibit better school bonding was associated with fewer reported risk behaviours both for students from high and low levels of adverse family relationships. These findings support the notion that a whole school approach targeted towards students, families and schools may be helpful in the prevention of risk behaviours.