Introduction The aim of this study was to highlight the perceived risks, behavioural changes and the rate of acceptance of seasonal and pandemic (H1N1) 2009 influenza vaccines by healthcare workers (HCWs) in a French Teaching Hospital. Methods We sampled HCWs from the Angers French Teaching Hospital (France) using a cross-sectional intercept design during phase 5A of the 2009 French National Plan for the Prevention and Control of ‘Pandemic Influenza’. From November 2009 to February 2010, HCWs were approached in the workplace to undertake the survey. The primary endpoint assessed immunization coverage among HCWs who had contact with at-risk-patients. Results Of the 532 HCWs who answered the questionnaire, 119 (22.4%) had received a seasonal vaccine and 194 (36.5%) the H1N1 pandemic vaccine. Coverage rate was significantly higher among physicians (45% for the seasonal vaccine, 61% for the H1N1 vaccine). The main reasons given for acceptance of the seasonal vaccine were “protection of the patient” and “self-protection”, whereas the main arguments against were “low risk of being infected” and “doubts about vaccine safety”. For the H1N1 vaccine, reasons for vaccination were to “protect the patient” and “protect the family”. The main arguments against were “fear of side effects” and “doubts about vaccine safety”. Conclusion This study emphasizes the lack of perception by HCWs of the importance of being immunized against seasonal and pandemic A (H1N1) 2009 Influenza. In the future, particular efforts are needed, during vaccination campaigns, to provide more information to HCWs regarding development process and safety of such vaccines.