Following the recent avian influenza and pandemic (H1N1) 2009 outbreaks, public trust in medical and political authorities is emerging as a new predictor of compliance with officially recommended protection measures. In a two-wave longitudinal survey of adults in French-speaking Switzerland, trust in medical organizations longitudinally predicted actual vaccination status 6 months later, during the pandemic (H1N1) 2009 vaccination campaign. No other variables explained significant amounts of variance. Trust in medical organizations also predicted perceived efficacy of officially recommended protection measures (getting vaccinated, washing hands, wearing a mask, sneezing into the elbow), as did beliefs about health issues (perceived vulnerability to disease, threat perceptions). These findings show that in the case of emerging infectious diseases, actual behavior and perceived efficacy of protection measures may have different antecedents. Moreover, they suggest that public trust is a crucial determinant of vaccination behavior and underscore the practical importance of managing trust in disease prevention campaigns.