Many children are treated for mental health disorders in primary care settings. The system of care (SOC) provides a framework for collaboration among pediatric mental health providers, but it is unclear if youth treated for mental health disorders in primary care receive such coordination. At the South Boston Community Health Center from September /2012 to August 2013 for 74 individuals ≤18 years, the odds of contact with SOC agencies (mental health, education, child protective services, juvenile justice and developmental disabilities) were compared for mental health treatment in primary versus specialty care. The odds of SOC contact within primary care were lower compared to specialty care (OR = 0.43, 95% CI = 0.29-0.66), specifically for mental health (OR = 0.54, 95% CI = 0.25-1.2), education (OR = 0.12, 95% CI = 0.050-0.28), and child protective services (OR = 0.64, 95% CI = 0.22-1.9). As care coordination may improve health outcomes, increased support and education for care coordination specific to youth treated for mental health disorders in primary care settings may be warranted.