Objectives: The importance of adolescent engagement in health decisions and public health programs such as immunisation is becoming increasingly recognised. Understanding adolescent preferences and further identifying barriers and facilitators for immunisation acceptance is critical to the success of adolescent immunisation programs. This study applied a discrete choice experiment (DCE) to assess vaccination preferences in adolescents. Methods: This study was conducted as a cross-sectional, national online survey in Australian adolescents. The DCE survey evaluated adolescent vaccination preferences. Six attributes were assessed including disease severity, target for protection, price, location of vaccination provision, potential side effects and vaccine delivery method. A mixed logit model was used to analyse DCE data. Results: This survey was conducted between December 2014 and January 2015. Of 800 adolescents aged 15 to 19 years, stronger preferences were observed overall for: vaccination in the case of a life threatening illness (p<0.001), lower price vaccinations (p<0.001), mild but common side effects (p = 0.004), delivery via a skin patch (p<0.001) and being administered by a family practitioner (p<0.001). Participants suggested that they and their families would be willing to pay AU$394.28 (95%CI: AU$348.40 to AU$446.92) more for a vaccine targeting a life threatening illness than a mild-moderate illness, AU$37.94 (95%CI: AU$19.22 to AU$57.39) more for being vaccinated at a family practitioner clinic than a council immunisation clinic, AU$23.01 (95%CI: AU$7.12 to AU$39.24) more for common but mild and resolving side effects compared to rare but serious side effects, and AU$51.80 (95%CI: AU $30.42 to AU$73.70) more for delivery via a skin patch than injection. Conclusions: Consideration of adolescent preferences may result in improved acceptance of, engagement in and uptake of immunisation programs targeted for this age group.