We analyzed data from a large randomized HIV/HCV prevention intervention trial with young injection drug users (IDUs) conducted in five U.S. cities. The trial compared a peer education intervention (PEI) with a time-matched, attention control group. Applying categorical latent variable analysis (mixture modeling) to baseline injection risk behavior data, we identified four distinct classes of injection-related HIV/HCV risk: low risk, non-syringe equipment-sharing, moderate-risk syringe-sharing, and high-risk syringe-sharing. The trial participation rate did not vary across classes. We conducted a latent transition analysis using trial baseline and 6-month follow-up data, to test the effect of the intervention on transitions to the low-risk class at follow-up. Adjusting for gender, age, and race/ethnicity, a significant intervention effect was found only for the high-risk class. Young IDU who exhibited high-risk behavior at baseline were 90 % more likely to be in the low-risk class at follow-up after the PEI intervention, compared to the control group.