BackgroundFew researchers have the data required to adequately understand how the school environment impacts youth health behaviour development over time.Methods/DesignCOMPASS is a prospective cohort study designed to annually collect hierarchical longitudinal data from a sample of 90 secondary schools and the 50,000+ grade 9 to 12 students attending those schools. COMPASS uses a rigorous quasi-experimental design to evaluate how changes in school programs, policies, and/or built environment (BE) characteristics are related to changes in multiple youth health behaviours and outcomes over time. These data will allow for the quasi-experimental evaluation of natural experiments that will occur within schools over the course of COMPASS, providing a means for generating “practice based evidence” in school-based prevention programming.DiscussionCOMPASS is the first study with the infrastructure to robustly evaluate the impact that changes in multiple school-level programs, policies, and BE characteristics within or surrounding a school might have on multiple youth health behaviours or outcomes over time. COMPASS will provide valuable new insight for planning, tailoring and targeting of school-based prevention initiatives where they are most likely to have impact.