Prior to its application for in vitro toxicological assays, thorough characterization of a cell line is essential. The present study uses global transcriptional profiling to characterize a lung epithelial cell line (FE1) derived from MutaMouse [White, P.A., Douglas, G.R., Gingerich, J., Parfett, C., Shwed, P., Seligy, V., Soper, L., Berndt, L., Bayley, J., Wagner, S., Pound, K., Blakey, D., 2003. Development and characterization of a stable epithelial cell line from Muta Mouse lung. Environmental and Molecular Mutagenesis 42, 166-184]. Results presented here demonstrate the origin of the FE1 lung cell line as epithelial, presenting both type I and type II alveolar phenotype. An assessment of toxicologically-relevant genes, including those involved in the response to stress and stimuli, DNA repair, cellular metabolism, and programmed cell death, revealed changes in expression of 22-27% of genes in one or more culture type (proliferating and static FE1 cultures, primary epithelial cultures) compared with whole lung isolates. Gene expression analysis at 4 and 24h following benzo(a)pyrene exposure revealed the induction of cyp1a1, cyp1a2, and cyp1b1 in FE1 cells and lung isolates. The use of DNA microarrays for gene expression profiling allows an improved understanding of global, coordinated cellular events arising in cells under different physiological conditions. Taken together, these data indicate that the FE1 cell line is derived from a cell type relevant to toxic responses in vivo, and shows some similarity in response to chemical insult as the original tissue.