Background Vaccination against seasonal influenza in health workers is recommended but coverage is variable. This study aimed to determine coverage of influenza vaccination among health workers in Lima, Peru in 2010; explore barriers and enabling elements for vaccination; and suggest strategies to improve coverage. Methods Qualitative interviews informed the development of a survey instrument that consisted of open and close-ended questions. Sub-analyses were done by occupational group and results were calculated as percentages for each possible response with confidence intervals of 95%. Results Coverage of the influenza vaccination was 77.2%. Vaccinated staff were less likely to have permanent contracts (p = 0.0150) and vaccination coverage was lower in physicians (p = 0.0001). Over 90% cited protection of themselves, families and patients as reasons for vaccination and 48% mentioned peer encouragement. Fear of adverse events (47%) and organizational barriers (>30%) were reasons for non-vaccination. To improve coverage, highest priority was given to strategies providing more information. Conclusions Key factors in driving health worker vaccination include desire for protection and peer encouragement. Perceptual barriers based on a misunderstanding of the epidemiology of influenza and vaccination could be overcome by targeted education and information. Organizational barriers require attention to how vaccination is implemented within health facilities.