Acylcarnitine analysis using tandem mass spectrometry has become a powerful tool in the investigation of pediatric patients presenting with clinical signs and symptoms suggestive of fatty acid oxidation defects. These signs are diverse and include failure to thrive, feeding difficulties, and cardiomyopathy. Because the signs and symptoms are nonspecific, the identification of acylcarnitines characteristic of these inherited diseases is necessary for diagnosis. We describe a method for the analysis of acylcarnitines in plasma or serum samples using electrospray ionization tandem mass spectrometry.