To identify the expression of genes that are regulated during adipocyte differentiations, the gene expression patterns in 3T3-L1 preadipocytes and mature 3T3-L1 adipocytes were compared with mRNA differential display. The expression of 56 genes was distinctively regulated, 40 were up- regulated while 16 were down-regulated in differentiated adipocytes. DNA sequences analyses indicate that differentiation of adipocytes was associated with a complex array of gene expression involving diverse biological functions, including DNA remodeling/transcription, cytoskeletal/ extracellular matrix proteins, insulin/growth factor signaling, lipid metabolism, mitochondrial functions, and adipocyte secretory trafficking. Among these genes, 34% (19 of 56) were also regulated by the PPARγ agonist BRL49653, a potent stimulator for adipocyte differentiation, suggesting that BRL/49653 effects on gene expression programming of adipocyte differentiation is unique and selective. These results provide novel insight into the regulation of gene expression programming during adipocyte differentiation and the control by PPARγ.