BACKGROUND: Aboriginal adolescents are more likely to become pregnant and contract an STI than other Canadian adolescents. This study provides some of the first data on factors associated with these outcomes among Aboriginal adolescents. METHODS: A secondary analysis was conducted using 2003 data from a large cross-sectional survey of British Columbia secondary school students. 445 young women and 360 young men who identified as Aboriginal and reported ever having sex were included in analyses. Associations between self-reported pregnancy and STI and 11 exposure variables were examined using logistic regression. RESULTS: Of young women, 10.6% reported a pregnancy; 10.5% of young men reported causing a pregnancy. An STI diagnosis was reported by 4.2% of young women and 3.9% of young men. In multivariate analyses for young men, ever having been sexually abused was the strongest consistent risk factor for causing a pregnancy (AOR = 4.30, 95% CI 1.64-11.25) and STI diagnosis (AOR = 5.58, 95% CI 1.61-19.37). For young women, abuse was associated with increased odds of pregnancy (AOR = 10.37, 95% CI 4.04-26.60) but not STI. Among young women, substance use was the strongest consistent risk factor for both pregnancy (AOR = 3.36, 95% CI 1.25-9.08) and STI (AOR = 5.27, 95% CI 1.50-18.42); for young men, substance use was associated with higher odds of STI (AOR = 4.60, 95% CI 1.11-19.14). Factors associated with decreased risk included community, school and family involvement. CONCLUSIONS: Health care professionals, communities and policy-makers must urgently address sexual abuse and substance use. Exploring promotion of school and community involvement and family cohesion may be useful for sexual health interventions with Aboriginal students.