Background: Health promotion policies targeting risk-taking behaviors are being implemented across schools in Israel. This study identified the most effective components of these policies influencing cigarette smoking and alcohol consumption among adolescents. Methods: Logistic hierarchical linear model (HLM) analysis of data for 5279 students in 95 Jewish public schools from the Health Behavior in School-Aged Children (HBSC) 2010-2011 survey in Israel enabled simultaneous estimation of the relationship between student- and school-level variables (health promotion policy) to alcohol consumption and smoking behavior. Principals of participating schools also were interviewed to ascertain their degree of adoption and implementation of a health promotion policy. Results: Most of the variance in adolescent risk behaviors is explained by student-level variables: negative perceptions of school, lack of parental support for school issues, and more time spent with friends. Among the school-level policy measures, parental participation in health promotion intervention programs was repeatedly associated with lower rates of risk behaviors, over and above student characteristics. Conclusions: School health promotion policies should focus on parents' involvement in intervention programs and should seek to improve students' perceptions of school and their sense of well-being to promote resilience. Further research is needed to identify additional factors that may increase the effectiveness of school health promotion policies.