Lactation and fasting are two physiological models characterized by negative energy balance. Our previous studies demonstrated that uncoupling protein (UCP) 3 expression in skeletal muscle was down-regulated during lactation and up-regulated during fasting. The present studies used cDNA microarray and real-time PCR to perform a systems and comparative analysis in gene expression in skeletal muscle under conditions of negative energy balance. Gastrocnemius skeletal muscle RNA pools were generated from the following groups of rats: cycling diestrous females, cycling females with 48 h of fasting, lactation, and lactation + leptin. Of those known genes studied, 35 genes were up-regulated and 49 were down-regulated during lactation. Leptin treatment during lactation reversed the differential regulation of about 80% of these genes, demonstrating the importance of the leptin suppression to the changes in skeletal muscle metabolism. GenMAPP analysis revealed a coordinated regulation at key steps in glycolysis/gluconeogenesis, the tricarboxylic acid cycle, and lipid metabolism, indicating an increased rate of lactate production through glycolysis and reduced fatty acid degradation in skeletal muscle during lactation. Particular interest was paid to those genes that changed in a similar manner to UCP3 mRNA. Many of these genes that were decreased during lactation and increased during fasting are involved in fatty acid degradation and transport, including acyl-coenzyme A dehydrogenase for medium chain fatty acid, carnitine palmitoyltransferase 1, and fatty acid translocase. The current studies provide a basis for investigating the mechanisms underlying metabolic adaptations during lactation and fasting and highlight the importance of UCP3 in lipid metabolism.