Abnormally high rates of fatty acid metabolism is an important contributor to the severity of ischemic heart disease. During and following myocardial ischemia a number of alterations in fatty acid oxidation occur that result in an excessive amount of fatty acids being used as a fuel source by the heart. This contributes to a decrease in cardiac efficiency both during and following the ischemic episode. Central to the regulation of fatty acid oxidation in the heart is malonyl CoA, which is a potent endogenous inhibitor of mitochondrial fatty acid uptake. The levels of malonyl CoA are regulated both by its synthesis by acetyl CoA carboxylase (ACC) and its degradation by malonyl CoA decarboxylase (MCD). ACC is in turn controlled by AMP-activated protein kinase (AMPK), which acts as a fuel gauge in the heart. The control of these enzymes are altered during ischemia, such that malonyl CoA levels in the heart decrease, resulting in an increased relative contribution of fatty acids to oxidative metabolism. Activation of AMPK during and following ischemia appears to be centrally involved in this decrease in malonyl CoA. Clinical evidence is now accumulating that show that inhibition of fatty acid oxidation is an effective approach to treating ischemic heart disease. As a result, modulation of fatty acid oxidation by targeting the enzymes controlling malonyl CoA may be a novel approach to treating angina pectoris and acute myocardial infarction. This paper will discuss some of the molecular changes that occur in fatty acid oxidation in the ischemic heart and will include a discussion of the important role of malonyl CoA in this process.