The airway epithelium is comprised of specialized cell types that play key roles in protecting the lungs from environmental insults. The cellular composition of the murine respiratory epithelium is established during development and different cell types populate specific regions along the airway. Here we show that E2f4-deficiency leads to an absence of ciliated cells from the entire airway epithelium and the epithelium of the submucosal glands in the paranasal sinuses. This defect is particularly striking in the nasal epithelium of E2f4-/- mice where ciliated cells are replaced by columnar secretory cells that produce mucin-like substances. In addition, in the proximal lung, E2f4 loss causes a reduction in Clara cell marker expression indicating that Clara cell development is also affected. These defects arise during embryogenesis and, in the nasal epithelium, appear to be independent of any changes in cell proliferation, the principal process regulated by members of the E2f family of transcription factors. We therefore conclude that E2f4 is required to determine the appropriate development of the airway epithelium. Importantly, the combination of no ciliated cells and excess mucous cells can account for the chronic rhinitis and increased susceptibility to opportunistic infections that causes the postnatal lethality of E2f4 mutant mice.