This study investigated the effectiveness of a school-based health program for Indigenous Australian students in Brisbane, between April and October 2013. The Deadly Choices? health education program was delivered weekly at 6 education facilities to participants from years 7 to 12 over 7 weeks. One school that received the Deadly Choices program the following term acted as the control group. All participants were surveyed immediately prior to and after the intervention to assess its impact upon knowledge, attitudes, self-efficacy and behaviours in relation to chronic disease and associated risk factors. Participants within the intervention group reported mostly significant improvements over time for questions relating to knowledge, attitudes and self-efficacy regarding leadership, chronic disease and risk factors. They also reported significant changes in regard to 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; considerably more improvements were observed 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.