Malonyl-CoA acts a fuel sensor in the pancreas, liver and muscle. Similarly, malonyl-CoA is implicated in satiety regulation in the brain. Expression of genes encoding enzymes implicated in regulation of malonyl-CoA levels was examined in murine brain. Acetyl-CoA carboxylase (ACC) alpha-isoform, fatty acid synthase and malonyl-CoA decarboxylase are highly expressed in the hippocampus, habenula nucleus, cerebral cortex and areas of the hypothalamus, whereas the ACC-beta isoform and liver-type carnitine palmitoyltransferase I (CPTI-L) are principally expressed in the choroid plexus. Thus different brain regions appear to be functionally configured primarily for either fatty acid synthesis or beta-oxidation. Localization of transcripts encoding enzymes involved in fatty acid synthesis and beta-oxidation in distinct nuclei of the hypothalamus supports a role for malonyl-CoA as a potential effector of satiety.