Vaccines are leading pharmacological measures for limiting the impact of pandemic influenza in the community. The objective of this study was to investigate the effectiveness of influenza (pandemic and seasonal) vaccines in preventing pandemic influenza-associated hospitalization. We conducted a multicenter matched case-control study in 36 Spanish hospitals. Patients hospitalized with confirmed pandemic influenza between November 2009 and February 2010 and two hospitalized controls per case, matched according to age, date of hospitalization and province of residence, were selected. Multivariate analysis was performed using conditional logistic regression. Subjects were considered vaccinated if they had received the vaccine >14 days (seasonal influenza vaccine) or >7 days (pandemic influenza vaccine) before the onset of symptoms (cases) or the onset of symptoms of the matched case (controls). For the pandemic influenza vaccine, vaccination effectiveness (VE) was estimated taking into account only patients recruited from November 23, 2009, seven days after the beginning of the pandemic influenza vaccination campaign. 638 cases and 1250 controls were included. The adjusted VE of the pandemic vaccine in the ≥18 years age group was 74.2% (95% CI, 29-90) and that of the influenza seasonal vaccine 15.0% (-34 to 43). The recommendation of influenza vaccination should be reinforced as a regular measure to reduce influenza-associated hospitalization during pandemics and seasonal epidemics.