Because of influenza vaccine shortages during the 2004-2005 influenza season, vaccine was targeted for high-risk priority groups. To assess among primary care physicians: (1) ability to identify priority patients; (2) extent of shortages; and (3) effects of shortages on vaccine redistribution, patient referral and future plans for vaccine delivery. Mailed surveys of pediatric (Peds), family medicine (FM), and general internal medicine (GIM) physicians randomly selected from the American Medical Association master file. Response rate was 37% and the study population included 377 Peds, 319 FM, and 251 GIM physicians. Seventy-five percent of Peds, 58% of FM and 60% of GIM had some method to identify priority patients, although only 39%, 21%, and 18%, respectively, had a computerized method. Forty-five percent of Peds, 73% of FM, and 75% of GIM experienced shortages, for a median of 2-3 months. Approximately 48%-50% of Peds, FM, and GIM obtained additional influenza doses; among these, 53% received vaccine from a public health entity. Fifty-one percent of Peds, 79% of FM, and 80% of GIM referred high-risk patients for immunization, 94% of the time to a public health clinic. More than 95% planned to administer influenza vaccine next season. The majority of physicians experienced influenza vaccine shortages for prioritized patients, especially those providers caring for adults. There was significant vaccine redistribution and patient referral, primarily involving the public health system. Enhancing methods of targeting priority patients and increasing cooperation with public health entities should be priorities in dealing with future influenza vaccine shortages.