The purpose of our study was to use a genome-wide approach to define the innate immune response of human AM to influenza. Using H1N1 influenza virus PR/8, we performed gene profiling of virus-infected human AM at 4 and 24 h post inoculation (hpi) and verified the alterations in IFN-related genes by real-time RT-PCR and cytokine response by ELISA. We investigated the kinetics of infection-induced cytokine response in human primary AM infected with both live and UV-inactivated PR/8 and the contemporary H3N2 virus A/New York/238/2005 (NY/238) [23] . We also determined if the cytokine response was amplified by paracrine proinflammatory cytokines, TNF-a and IL-1b. In addition, we explored whether influenza infection diminishes gene expression of macrophage scavenger receptors, which could contribute to the impaired ability of AM to clear other pathogens after influenza.