Youth with severe emotional and behavioral disorders (EBD) were randomly assigned for 3 months of intensive treatment to a 5-day residential program (5DR Program) or a community-based alternative, family preservation program (FP Program). Programs differed not only in method of service delivery (residential unit vs. home-based), but also in treatment philosophy (solution focused brief therapy vs. cognitive behavioral). Results confirmed high rates of comorbidity in this population for externalizing and internalizing disorders. A significant Treatment x Program interaction was evident for internalizing disorders. At 1-year follow-up, significantly higher percentages of youth from the FP Program revealed a reduction of clinical symptoms for ADHD, as well as, general anxiety and depression, whereas significant proportion of youth from the 5DR Program demonstrated clinical deterioration and increased symptoms of anxiety and depression. Results have implications for future treatment of youth with EBD and suggest that greater emphasis be placed on research linking treatment to specific symptom clusters, especially highly comorbid clusters in this hard to serve population.