Without insight into the primary care environment, further improvements in influenza immunization rates are unlikely. We conducted a comparative case study of family medicine offices during the 2003 influenza immunization season. Practice 1 (P1) served an urban African American population, practice 2 (P2) served a suburban non-minority population, practice 3 (P3) served an urban Hispanic population. Influenza immunization rates among patients age 65 years and older in P1, P2, and P3 were 32%, 33%, and 67% by medical chart. Rates were highest in P3, where medical staff supported vaccination, promoted communication with patients and staff, and made use of systems to identify eligible patients. Characteristics that appear to affect influenza immunization in the primary care environment include the presence of a practice champion, issues of communication and collaboration, and the use of systems approaches. These data support the need for investigation of how these factors affect population level disparities.