The development of the fetal lung is a complex biological process, which involves temporal and spatial regulations of many genes. In order to understand the molecular mechanisms of this process, we investigated gene expression profiles of the fetal lungs on gestational days 18, 19, 20, 21, as well as the lungs of new born and adult rats. For this analysis, we used in-house rat DNA microarray containing 6,000 known genes and 4,000 expressed sequence tags (ESTs). 1,512 genes passed the statistical SAM test and 583 genes (402 known genes and 181 ESTs) had a 2-fold change at least between two time points. K-means cluster analysis revealed 7 major expression patterns. In one of the clusters, gene expression increased from day 18 to 20 and thereafter decreased. This cluster contained 10 known genes and 5 ESTs; 8 of them are associated with development. Real-time PCR analysis of these 10 genes showed an 88% consistency with the microarray data. The mRNA of lim homeodomain protein 3a (Lhx3), a transcription factor, was enriched in fetal type II cells. In contrast, pleiotrophin (Ptn), a growth factor, had a much higher expression in fetal lung tissues than in fetal type II cells. Immunohistochemistry revealed that Lhx3 was localized in fetal lung epithelial cells and Ptn in the mesenchymal cells adjacent to the developing epithelium and blood vessel. Furthermore, using GenMAPP, we identified 4 regulatory pathways: TGF beta signaling, inflammatory response, cell cycle, and G protein signaling. We also identified 2 metabolic pathways: glycoysis and gluconeogenesis, and proteasome degradation. Our results may provide new insights into the complex regulatory pathways that control fetal lung development.