Gene therapy targeted at the respiratory epithelium holds therapeutic potential for diseases such as cystic fibrosis and alpha-1 anti-trypsin deficiency. A variety of approaches such as intranasal or intratracheal instillation and aerosol delivery have been utilized to target genes to the airways. Polyethylenimine (PEI), a linear or branched polycationic polymer, has been used for delivery of genes to various organs. In this study, using fluorescein isothiocyanate (FITC)-labeled branched PEI, we initially examined the localization of PEI in the lungs after aerosol delivery to Balb/C mice. Further, after aerosol delivery of PEI-CAT DNA, in situ immunostaining for chloramphenicol acetyl transferase (CAT) protein was used to localize the transgene expression within the lungs. Immunohistochemistry for CAT, as well as localization of FITC-labeled PEI, revealed that after aerosol delivery, the PEI-DNA complexes deposit and subsequently transfect most of the epithelial cells in the conducting airways (including the peripheral airways). High levels of CAT were detected at 24 h after aerosol exposure and significant CAT expression was detected in the lungs up to 28 days after a single aerosol exposure. The data suggest that aerosol delivery of PEI-DNA complexes could be effective for the treatment of pulmonary diseases such as cystic fibrosis and alpha-1 anti-trypsin deficiency.