To evaluate the role of cell-mediated immunity during gene transfer to the respiratory epithelium, the time course of luciferase activity was assessed after intratracheal administration of Av1Luc1, an E1a-E3-deleted adenoviral (Ad5) vector expressing firefly luciferase, to FVB/N, BALB/c and BALB/c-nu/nu adult mice. Adenovirus-mediated luciferase activity was rapidly lost from the respiratory tract between 2 and 14 days after treatment of both FVB/N and BALB/c wild-type mice. In the wild-type mice, loss of luciferase activity was associated with an early inflammatory response consisting of infiltration with macrophages and polymorphonuclear leukocytes and a more prolonged response characterized by lymphocytic infiltration. In the immune-deficient nu/nu mice, luciferase activity was maintained at higher levels than in immune-competent mice after exposure to virus and was associated with a distinct pattern of inflammation, consisting primarily of macrophages and polymorphonuclear cells but lacking the lymphocytic infiltrates typical of the inflammation in wild-type mice. Adenoviral DNA was rapidly cleared from the lungs of both nu/nu and wild-type mice. Markedly increased expression of proliferating cell nuclear antigen (PCNA) was observed in bronchiolar and alveolar epithelial cells and in inflammatory cells after exposure to Av1Luc1. The proliferative response of the respiratory epithelium was more extensive and persistent in wild-type than in nu/nu mice. To assess further the impact of the immune system on adenovirus-mediated gene expression, cotton rats treated with cyclosporin A or dexamethasone were exposed to Av1Luc1. Both agents decreased lung inflammation and significantly increased lung luciferase activity. The loss of lung luciferase activity is dependent, in part, on the immune-mediated clearance of respiratory epithelial cells, which may limit the extent and duration of gene expression with recombinant adenoviral vectors.