Abstract: The aim of this study was to investigate the effectiveness of a school-based health promotion and education program in improving knowledge, attitudes, self-efficacy and behaviours of urban Indigenous young people regarding chronic disease and associated risk factors. A mixed methods approach was adopted for this evaluation; however, this paper will focus on the quantitative aspect of the study. The Deadly Choices™ health education program was delivered weekly at six education facilities in Brisbane, Australia to participants from years seven to 12 over seven weeks. One school that received the Deadly Choices program the following term acted as the control group. Questionnaire data was collected immediately pre and post intervention to assess program impact. As self-reported by participants there were mostly significant improvements over time for questions relating to knowledge, attitudes and self-efficacy regarding leadership, chronic disease and risk factors within the intervention group. There were also significant changes within the intervention group regarding breakfast frequency (P = 0.002), physical activity frequency (P ≤ 0.001), fruit (P = 0.004) and vegetable (P ≤ 0.001) intake. Overall, there were few significant differences between the control and intervention groups regarding health attitudes and behaviours; however, there were considerably more improvements relating to self-efficacy and knowledge of chronic disease and associated risk factors between groups. The program also facilitated 30 Aboriginal and Torres Strait Islander health checks for participants. Deadly Choices is an innovative and comprehensive school-based program which has great potential to improve the health outcomes of Indigenous young people in urban areas by providing education in leadership and chronic disease prevention; engaging students in physical activity participation; and collaborating with health services to facilitate health checks.