Alveolar epithelial type I and type II cells (AEC I and II) are closely aligned in alveolar surface. There is much interest in the precise identification of AEC I and II in order to separate and evaluate functional and other properties of these two cells. This study aims to identify specific AEC I and AEC II cell markers by DNA microarray using the in vitro trans-differentiation of AEC II into AEC I-like cells as a model. Quantitative real-time PCR confirmed five AEC I genes: fibroblast growth factor receptor-activating protein 1, aquaporin 5, purinergic receptor P2X 7 (P2X7), interferon-induced protein, and Bcl2-associated protein, and one AEC II gene: gamma-aminobutyric acid receptor pi subunit (GABRP). Immunostaining on cultured cells and rat lung tissue indicated that GABRP and P2X7 proteins were specifically expressed in AEC II and AEC I, respectively. In situ hybridization of rat lung tissue confirmed the localization of GABRP mRNA in type II cells. P2X7 and GABRP identified in this study could be used as potential AEC I and AEC II markers for studying lung epithelial cell biology and monitoring lung injury.