Ghrelin is a gastric hormone increased during caloric restriction and fat depletion. A role of ghrelin in the regulation of lipid and energy metabolism is suggested by fat gain independent of changes in food intake during exogenous ghrelin administration in rodents. We investigated the potential effects of peripheral ghrelin administration (twice-daily 200-µg subcutaneous injection for four days) on triglyceride content and mitochondrial and lipid metabolism gene expression in rat liver and muscles. Compared to vehicle, ghrelin increased body weight but not food intake and circulating insulin. In liver ghrelin induced a lipogenic and glucogenic pattern of gene expression and increased triglyceride content while reducing activated (phosphorylated) stimulator of fatty acid oxidation AMP-activated protein kinase (AMPK) (all P<0.05) with unchanged mitochondrial oxidative enzyme activities. In contrast triglyceride content was reduced (P<0.05) following ghrelin administration in mixed (gastrocnemius) and unchanged in oxidative (soleus) muscle. In mixed muscle ghrelin increased (P<0.05) mitochondrial oxidative enzyme activities independent of changes in expression of fat metabolism genes and phosphorylated AMPK. Expression of peroxisome proliferative-activator receptor (PPAR)- whose activation reduces muscle fat content was selectively increased in mixed muscle where it paralleled changes in oxidative capacities (P<0.05). Thus ghrelin induces tissue-specific changes in mitochondrial and lipid metabolism gene expression and favors triglyceride deposition in liver over skeletal muscle. These novel effects of ghrelin in the regulation of lean tissue fat distribution and metabolism could contribute to metabolic adaptation to caloric restriction and loss of body fat.