Little is known about the organizational contexts associated with different primary care (PC) approaches to managing PC patients with drinking problems. Relying upon the Chronic Care Model and a theoretically based taxonomy of health care systems, we identified organizational factors distinguishing PC practices using PC-based approaches (managed by PC providers, mental health specialists, or jointly with specialty services) versus referral-based management in the Veterans Affairs health care system. Data were obtained from a national survey of 218 PC practices characterizing usual management approaches as well as practices' leadership, delivery system design, information system, and decision support characteristics and from a national survey of substance use disorder specialty programs. PC- and referral-based practices did not differ on the sufficiency of their structural resources, physician staffing, or on the availability of specialty services. However, PC-based practices were found to take more responsibility for managing patients' chronic conditions and had more staff for decision support activities.