Malonyl-CoA decarboxylase deficiency is an inborn error of metabolism that may cause hypotonia and a fatal cardiomyopathy in infancy. Newborn metabolic screening programs do not include this disorder, although there is a possibility that presymptomatic treatment may attenuate the development of cardiomyopathy. We report a case of malonyl-CoA decarboxylase deficiency in a 5-month-old boy who presented with cardiomyopathy and hypotonia. Retrospective analysis of the newborn screening test showed an elevation in the concentration of malonylcarnitine at age 3 days. Unfortunately, this perturbation was missed because the screening test did not routinely measure malonylcarnitine in the newborn blood. Our experience confirms the possibility of screening for malonyl-CoA decarboxylase deficiency with tandem mass spectrometry. This finding should enable studies to determine if presymptomatic treatment could change the outcome in this often fatal disorder.