INTRODUCTION: During the past decade, the number of Aboriginal people diagnosed with HIV in Canada has grown more than any other ethnicity. Whereas the majority of infections are related to injection drug use, factors that explain elevated risk and transmission of HIV among Aboriginal young people who use illicit drugs are not well understood. STUDY DESIGN: Observational study. METHODS: The Cedar Project is an observational study of Aboriginal youth living in Vancouver and Prince George, BC. Eligibility criteria include age (14-30 years) and self-reported use of non-injection or injection drugs at least once in the month before enrolment. Between October 2003 and April 2005, 512 participants were recruited and completed a questionnaire administered by an Aboriginal interviewer. Multivariable logistic regression analysis was used to model the independent association of demographic and behavioural variables of individuals with HIV infection. RESULTS: Of the participants, 235 resided in Prince George and 277 in Vancouver. Among the 276 participants that used injection drugs, HIV prevalence was significantly higher in Vancouver (17% vs. 7%) but HCV prevalence was higher in Prince George (62% vs. 57%). In Vancouver, 40% of injectors reported daily heroine use compared with 12% in Prince George. In contrast, Prince George participants were more likely to report daily injection of cocaine compared with those in Vancouver (37% vs. 21%). A higher percentage of Prince George participants reported having difficulty accessing clean syringes (22% vs. 8%). History of non-consensual sex, residing in Vancouver and duration of injection drug use were independent factors associated with increased risk of HIV infection. CONCLUSIONS: HIV and HCV prevalence are elevated in young Aboriginal drug users residing in Vancouver and Prince George. Heterogeneity exists in these locations with respect to drug of choice and access to clean syringes. Prevention and treatment programs are urgently required in this population.