Influenza virus infections usually cause mild to moderately severe respiratory disease, however some infections, like those involving the avian H5N1 virus, can cause massive viral pneumonia, systemic disease and death. The innate immune response of respiratory tract resident cells is the first line of defense and limits virus replication. Enhanced cytokine and chemokine production following infection, however, appears to underlie much of the pathology that develops after infection with highly pathogenic strains. A so-called `cytokine storm' can damage the lung tissue and cause systemic disease, despite the control of viral replication. By summarizing current knowledge of the innate responses mounted to influenza infection, this review highlights the importance of the respiratory tract epithelial cells as regulators of innate and adaptive immunity to influenza virus.