: Approximately 5% of adolescents in the US meet criteria for a substance use disorder (SUD), and many of them benefit from residential treatment programs at points in the course of the disorder to achieve early sobriety and stabilization. Youth with chronic medical conditions use alcohol, marijuana, and other substances at levels similar to peers, but are at greater risk of progression to heavy or problem use of alcohol, marijuana, and tobacco by young adulthood and often encounter unique treatment barriers that limit access to an appropriate level of care. We describe 2 such adolescents; a 15-year-old boy with type 1 diabetes who experienced interruptions in substance use treatment because of concerns regarding routine glycemic management and a 17-year-old boy with inflammatory bowel disease, who experienced treatment delays in the context of increasing alcohol and marijuana use because of digestive symptoms. For both of these adolescents, lack of access to professionals who could manage chronic medical conditions prevented delivery of substance use treatment and resulted in an increase in substance use behaviors. These cases illustrate the need for integrated substance use care within medical specialty settings. We propose opportunities for improvement, such as providing cross-training for medical and addiction treatment teams and integration of substance use treatment within traditional medical facilities.