Co-occurring mental illness and addiction is very common and results in worse treatment outcomes compared to singly diagnosed addicted individuals. Integrated treatment for co-occurring disorders is associated with better treatment outcomes; however there is a wide range of what is included in integrated treatment. Due to patient and staff interests, integrated treatment often includes complementary and alternative therapies, including music and art therapy. There is a need to study how these approaches effect treatment engagement, retention, and outcome. This study was a prospective naturalistic non-randomized pilot study without a control group that sought to evaluate how participation in a music therapy program affected treatment outcomes for individuals with co-occurring mental illness and addiction. In summary, music therapy appears to be a novel motivational tool in a severely impaired inpatient sample of patients with co-occurring disorders. Future studies of music therapy in integrated co-occurring disorder setting should include a control group.