Mucosal epithelial cells are an important component of the innate immune system forming a physical and immunologic barrier to inhaled bacteria. As polarized cells with tight junctions, the immunologic signaling functions of airway epithelial cells differ from those of professional immune cells. While many bacterial gene products activate airway mucosal cells, flagella are especially immunostimulatory. The motility function provided by flagella is essential for the initial stages of respiratory infection associated with opportunists such as Pseudomonas aeruginosa. Apically presented toll-like receptor 5 responds specifically to bacterial flagellin transducing a number of epithelial proinflammatory signaling cascades, including the induction of Ca2+ fluxes; activation of NF-kappaB, IL-8, and matrilysin; and mucin expression. The complexities of flagella and flagellin structures, how these bacterial components initiate host signaling and their potential as a vaccine target are reviewed.