The 2009 influenza pandemic (H1N1pdm) has completed its first wave in many northern and southern hemisphere populations and many northern hemisphere populations are reporting substantial activity indicating the start of a second wave this autumn. As the global epidemiology of this novel strain unfolds, substantial policy challenges will continue to present themselves for the next 12 to 18 months. Here, we anticipate six public health challenges and identify data that are required for public health decision making. In particular, we suggest studies that will generate data not otherwise available from routine surveillance. Representative serological surveys stand out as a critical source of data with which to reduce uncertainty around policy choices for both pharmaceutical and non-pharmaceutical interventions after the initial wave has passed. Also, monitoring the time course of incidence of severe H1N1pdm cases will give a clear picture of variability in underlying transmissibility of the virus during population wide changes in behavior such as school vacations and other non-pharmaceutical interventions. In addition, we address low resource settings where routine surveillance for influenza has not been established and suggest alternative ways to collect data for the 2009 (and beyond) influenza H1N1 pandemic.