A sample of 1,038 patients newly admitted to 15 methadone clinics in New York City were studied for up to three years in treatment or until discharge. Cluster analysis identified distinct patient groups with very different heroin and cocaine usage patterns during treatment. About 80% either started in or transitioned to a low heroin use group and 50% either started in or transitioned to a low cocaine use group during treatment. One-third of patients used cocaine extensively during treatment. Other "high risk" groups, such as those not recently employed, younger, or involved with criminal justice, could benefit from special interventions very early in treatment.