Uncontrolled apoptosis has been associated with several pulmonary disorders; however, the molecular mechanism underlying this process and the fate of apoptotic cells in vivo are unclear. Here we show that direct administration of apoptotic cells to the lungs of rats caused pulmonary inflammation and fibrosis, as indicated by emigration of inflammatory cells to the airspaces, TNF-immunoreactivity and connective tissue accumulation, indicating a direct relationship between apoptotic cells and the observed lung pathologies. To determine how the lungs process the accumulated apoptotic cells, normal or apoptotic cells from autologous donor rats were labeled with fluorescent nanobeads and intratracheally instilled into the lungs of rats. Probe distribution and lung cell apoptosis were determined at various times over a 28 days period using confocal fluorescence microscopy and terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling (TUNEL), respectively. Labeled apoptotic cells were cleared by lung macrophages within one week after the treatment. However, the total number of apoptotic cells in the lung remained high at 28 days post-treatment. The results indicate a continuous induction of secondary apoptosis by apoptotic cell instillation which may contribute to the observed lung pathology. Analysis of lung cell apoptosis by caspase assays showed an elevation of caspase-8 but not capase-9 in the treatment group at 28 days post-treatment, indicating involvement of the death receptor-mediated pathway in the apoptotic process. Together, our results demonstrate a direct effect of apoptotic cell accumulation on inflammatory and fibrotic pulmonary responses and the continuous induction of lung cell apoptosis by apoptotic cell instillation.