Despite experimental evidence supporting an adverse role for air pollution in models of human disease, little has been done in the way of assessing the health effects of inhalation of whole mixtures from defined sources at exposure levels relevant to ambient environmental exposures. The current study assessed the impact of inhaled diesel engine emissions (DEE) in modulating clearance of Pseudomonas aeruginosa (P.a.) and the adverse effects of infection to the pulmonary epithelium. At DEE concentrations representing from high ambient to high occupational exposures, mice were exposed to DEE continuously for one week or six months (6 h/day), and subsequently infected with P.a. by intratracheal instillation. At 18 h following P.a. infection, prior exposure to DEE impaired bacterial clearance and exacerbated lung histopathology during infection. To assess the airway epithelial cell changes indicative of lung pathogenesis, markers of specific lung epithelial cell populations were analyzed by immunohistochemistry. Both ciliated and non-ciliated airway epithelial cell numbers were decreased during P.a. infection by DEE exposure in a concentration-dependent manner. Furthermore, the lung transcription regulator, thyroid transcription factor 1 (TTF-1), was also decreased during P.a. infection by prior exposure to DEE concordant with changes in airway populations. These findings are consistent with the notion that environmental levels of DEE can decrease the clearance of P.a. and increase lung pathogenesis during pulmonary bacterial infection.