The recent H1N1 pandemic influenza stimulated numerous studies into the attitudes and intentions about the H1N1 vaccine. However, no study has investigated prospective predictors of vaccination behaviour. We conducted a two-wave longitudinal study among residents in four U.S. cities during the course of the H1N1 outbreak, using Internet surveys to assess demographic, cognitive and emotional predictors of H1N1 vaccination behaviour. Surveys were conducted at two time points, before (Time 1) and after (Time 2) the H1N1 vaccine was widely available to the public. Results show that Time 2 vaccination rates, but not Time 1 vaccination intentions, tracked H1N1 prevalence across the four cities. Receipt of seasonal influenza vaccine in the previous year, worry, compliance with recommended interventions, household size and education assessed at Time 1 were significant prospective predictors of vaccination behaviour. Perception of the H1N1 vaccine, social influence and prioritised vaccine recipient status assessed at Time 2 also predicted vaccination behaviour. Critically, worry about H1N1 mediated the effects of both objective risk (prevalence at the city level) and perceived risk on vaccination behaviour. These results suggest that H1N1 vaccination behaviour appropriately reflected objective risk across regions, and worry acted as the mechanism by which vaccination behaviour followed objective risk.