Leptin, a hormone secreted by adipose tissue, has been shown to have a major influence on hepatic lipid and lipoprotein metabolism. To characterize changes in lipid and lipoprotein gene expression in mouse liver, suppression subtractive hybridization and cDNA microarray analysis were used to identify mRNAs differentially expressed after leptin treatment of ob/ob mice. Ob/ob mice showed a profound decrease in mRNAs encoding genes controlling bile acid synthesis and transport as well as a variety of apolipoprotein genes and hepatic lipase with reversal upon leptin administration, suggesting that leptin coordinately regulates high density lipoprotein and bile salt metabolism. Leptin administration also resulted in decreased expression of genes involved in fatty acid and cholesterol synthesis, glycolysis, gluconeogenesis, and urea synthesis, and increased expression of genes mediating fatty acid oxidation, ATP synthesis, and oxidant defenses. The changes in mRNA expression are consistent with a switch in energy metabolism from glucose utilization and fatty acid synthesis to fatty acid oxidation and increased respiration. The latter changes may produce oxidant stress, explaining the unexpected finding that leptin induces a battery of genes involved in antioxidant defenses. Expression cluster analysis revealed responses of several sets of genes that were kinetically linked. Thus, the mRNA levels of genes involved in fatty acid and cholesterol synthesis are rapidly (<1 h) repressed by leptin administration, in association with an acute decrease in plasma insulin levels and decreased sterol regulator element-binding protein-1 expression. In contrast, genes participating in fatty acid oxidation and ketogenesis were induced more slowly (24 h), following an increase in expression of their common regulatory factor, peroxisome proliferator-activated receptor alpha. However, the regulation of genes involved in high density lipoprotein and bile salt metabolism shows complex kinetics and is likely to be mediated by novel transcription factors.