A simple radioisotopic assay for malonyl-CoA is described. The method is based on the malonyl-CoA-dependent incorporation of labeled acetyl-CoA into palmitic acid catalyzed by fatty acid synthetase in the presence of NADPH. Its main advantages over the more conventional spectrophotometric procedure is that it is extremely sensitive and allows the simultaneous determination of picomole quantities of malonyl-CoA in multiple tissue extracts. It should prove particularly suitable for studies on the regulation of lipid metabolism in isolated hepatocytes where the quantity of tissue available for analysis is frequently very small. Application of the method to the measurement of malonyl-CoA in livers from fed, fasted, and diabetic rats yielded values that were consistent with the recently postulated role of malonyl-CoA in the regulation of hepatic ketone body production.