To date, little is known regarding the spatio-temporal characteristics of the 2009 pandemic H1N1 as well as factors affecting the recovery of the infected patients in mainland China, especially for the initial cases, who were younger and more mobile than general population. The present study was therefore conducted to investigate the geographic distribution of H1N1 infection in the 2009 pandemic as well as the risk factors for adverse patient outcome after initial H1N1 virus infection in mainland China. Our goal was to generate solid scientific bases for adequate preparedness for potential H1N1 pandemic in the future.