Summary Objectives To investigate the factors associated with the uptake of influenza A/H1N1 vaccination by university students, and to examine the relationship between intention and actual vaccination. Study design Prospective cohort study. Methods A baseline survey was conducted among students at the Chinese University of Hong Kong in 2009 to collect data on demographics, pandemic risk perceptions and self-reported intention to be vaccinated in the future. A follow-up survey was conducted in 2011 using an online survey platform collecting information on actual vaccine uptake behaviour, and vaccine attitudes, knowledge and perceptions. Results Self-reported intention to be vaccinated in 2009 was significantly associated with actual vaccine acceptance. Vaccine perceptions (attitudes and knowledge) were found to be a better predictor of vaccine acceptance than disease risk perceptions. Being a medical or science student and receiving health advice about vaccination from a doctor or school-endorsed advertisement were also found to be predictors of vaccine acceptance. Conclusions University students in Hong Kong were wary of the A/H1N1 vaccination campaign, as revealed by their low uptake rate and doubts about the vaccine. Knowledge of the pandemic and vaccine was high in this population, but feelings of susceptibility were low. The results indicate a need to provide tailored messages emphasizing the importance of vaccination and the efficacy of the vaccine in the future.