Recently, a novel influenza A (H7N9) virus infected humans in China (1,2), leading to great concerns about its threat to public health (3). However, almost all the current genomes of the novel subtype H7N9 virus have been sequenced after culture in embryonated chicken eggs or mammalian cells. Switching the evolutionary selection pressure from in vivo human respiratory tract to embryonated chicken eggs might introduce mutations into the final genome sequences during culture (4). We report determination of the full genome of the influenza A (H7N9) virus derived directly by deep sequencing, without virus culture, from a sputum specimen of an infected human. Deep sequencing provides a direct way to evaluate the genome characteristics and potential virulence and transmissibility of the novel influenza A (H7N9) virus.