Tumor necrosis factor alpha (TNF-alpha) and other cytokines induce a state of negative energy balance leading to the breakdown of skeletal muscle. Leptin, another member of the cytokine superfamily, also induces a state of negative energy balance but does not alter lean body mass. The transcription profile of skeletal muscle was compared in animals treated with TNF-alpha or leptin or in animals pair-fed over a 7-day time course using 11,000-gene microarrays (Affymetrix, Santa Clara, CA). Ten clusters of skeletal muscle genes were identified, each of which showed significantly different expression between TNF-alpha treatment and pair feeding. Studies comparing leptin treatment and pair feeding revealed that both activate nearly identical programs of gene expression in skeletal muscle. These data indicate that the effects of leptin on skeletal muscle are markedly different from those of TNF-alpha and that the effects of leptin on skeletal muscle can be largely ascribed to its anorectic effects. Subtle differences between leptin and pair feeding were evident only after 7 days of treatment. In general, pair feeding altered gene expression after the 7-day treatment, whereas leptin did not. The effects of TNF-alpha on skeletal muscle are distinct from those of pair feeding, a result consistent with its known catabolic effects on this tissue. Analyses of the data from food-restricted animals also identified a set of transcriptional changes associated with this state. Further studies of many newly identified leptin-, TNF-alpha-, and starvation-regulated genes and the apparent coordinate regulation of these clusters may reveal important insights into the different effects of cytokines on skeletal muscle.