We have provided a detailed evaluation of how collaboration between an Ontario public health unit and its primary care providers facilitated an optimal response to the 2009 H1N1 influenza pandemic. Family health teams (integrated, interdisciplinary teams that provide a range of care options) provided flu assessment centers, with public health as a partner providing infection control advice, funding, coordination, antiviral medication, clinical care guidelines, supplemental nurse staffing, and arrangement of communication strategies with the public. The family health team structure offers a new capacity for timely, coordinated, and comprehensive response to public health emergencies, in partnership with public health, and provides a promising new direction for healthcare organization.