We report the case of a newborn infant with myocardial infarction caused by thromboembolic occlusion of the left main coronary artery. The clinical presentation was similar to that of hypoplastic left heart. This infant had no condition previously associated with perinatal myocardial infarction. Recognition and management of this rare condition, including the use of thrombolytic therapy, and the implication of deficient natural anticoagulant factors as a cause are discussed.