Hepatic stellate cells (HSCs) are activated by producing potentially injurious connective tissue components during hepatic fibrosis, thereby exerting a pivotal action in the development of liver fibrogenesis. The aim of this study was to investigate differences in gene expression patterns during the activation of HSCs using complementary cDNA microarrays. HSCs were isolated from normal rat livers and cultured for 0 (3 h), 3, 5 and 7 d. RNA was extracted from cultured cells at each point. The target RNA was hybridized to gene-specific sequence probes immobilized on chips. The hybridization signal was assessed using a confocal laser scanner Comparison of hybridization signals and patterns allows the identification of mRNAs that are expressed differentially. Statistical analysis was used to classify and cluster the genes according to their up- or downregulation. As a result, 33 upregulated early-stage and 36 upregulated late-stage gene candidates were identified. This time-based study revealed a number of newly discovered genes involved in fibrogenesis during the activation of HSCs.