OBJECTIVE Low rates of influenza immunization among health care workers (HCWs) pose a potential health risk to patients in primary care practices. Despite previous educational efforts and programs to reduce financial barriers, HCW influenza immunization rates remain low. Variation in practice-level organizational culture may affect immunization rates. To explore this relationship, we examined organizational cultures and HCWs' influenza immunization behaviors in three family medicine practices. METHODS We used a multi-method comparative case study. A field researcher used participant observation, in-depth interviews, and key informant interviews to collect data in each practice in November-December 2003. A diverse team used grounded theory to analyze text data. RESULTS Organizational culture varied among practices and differing HCW immunization rates were observed. The most structured and business-like practice achieved immunization of all HCWs, while the other two practices exhibited greater variation in HCW immunization rates. Physicians in the practices characterized as chaotic/disorganized or divided were immunized at higher rates than other members of the practices. CONCLUSIONS In these practices, organizational culture was associated with varying rates of influenza immunization for HCWs, especially among nonphysicians. Addressing elements of organizational culture such as beliefs regarding influenza immunization and office policies may facilitate the immunization of all staff members.