Influenza causes substantial morbidity and mortality annually, particularly in high-risk groups such as the elderly, young children, immunosuppressed individuals, and individuals with chronic illnesses. Healthcare-associated transmission of influenza contributes to this burden but is often under-recognized except in the setting of large outbreaks. The Centers for Disease Control and Prevention has recommended annual influenza vaccination for healthcare workers (HCWs) with direct patient contact since 1984 and for all HCWs since 1993. The rationale for these recommendations is to reduce the chance that HCWs serve as vectors for healthcare-associated influenza due to their close contact with high-risk patients and to enhance both HCW and patient safety. Despite these recommendations as well as the effectiveness of interventions designed to increase HCW vaccination rates, the percentage of HCWs vaccinated annually remains unacceptably low. Ironically, at the same time that campaigns have sought to increase HCW vaccination rates, vaccine shortages, such as the shortage during the 2004-2005 influenza season, present challenges regarding allocation of available vaccine supplies to both patients and HCWs. This two-part document outlines the position of the Society for Healthcare Epidemiology of America on influenza vaccination for HCWs and provides guidance for the allocation of influenza vaccine to HCWs during a vaccine shortage based on influenza transmission routes and the essential need for a practical and adaptive strategy for allocation. These recommendations apply to all types of healthcare facilities, including acute care hospitals, long-term-care facilities, and ambulatory care settings.