The Veterans Health Administration (VHA) serves a population at high risk of influenza-related morbidity and mortality. The national public health response to the vaccine shortage of the 2004-2005 season resulted in prioritization of recipients and redistribution of available supply. To characterize the impact of the 2004-2005 influenza vaccine shortage on vaccination among users of VHA facilities. Analysis using data from the cross-sectional VHA Survey of Healthcare Experiences of Patients. Outpatients seen in VHA clinics during the months September 2004-March 2005. Sociodemographics, vaccination prevalence, setting of vaccination, and reasons cited for not getting vaccinated. Influenza vaccination prevalence among VHA outpatients aged 50-64 was 56% and for those aged > or = 65 was 86%. Compared to the 2 previous seasons, this estimate was lower for patients age 50-64 but similar for patients > or = 65. After adjustment for patient characteristics, unvaccinated patients aged 50-64 were 8.3 (95% CI 6.0, 11.4) times as likely to cite that they were told they were not eligible for vaccination because of the national shortage compared to patients > or = 65. Regional VHA variation in vaccination receipt and shortage-related reasons for nonvaccination was small. The national influenza vaccine shortage of 2004-2005 primarily affected VHA users aged 50-64, consistent with the tiered prioritization guidance issued by the Centers for Disease Control and Prevention and Advisory Committee on Immunization Practices. Despite the shortage, vaccination prevalence among VHA users > or = 65 remained high.