At the cellular level, the respiratory tract has a variety of defense mechanisms to prevent bacterial infection. Recent data have demonstrated that the respiratory epithelium plays a very active role in host defense. In this review we start by examining the respiratory epithelia and its function in mucociliary clearance, and extend our review to include its role in the secretion and regulation of inflammatory cytokines and production of antimicrobial factors. Furthermore, we examine how recent advances in understanding cystic fibrosis have provided useful insights into the pathogenesis of lower respiratory tract infection. In addition, we examine how two common respiratory pathogens, Streptococcus pneumoniae and Pseudomonas aeruginosa, subvert the defense mechanisms at the cellular level. Finally, we attempt to identify new or potential therapeutic approaches that have arisen from some of the insights into the pathogenesis of lower respiratory tract infections.