Acylcarnitines are acetylated forms of L-carnitine derived from the breakdown of amino and fatty acids. Acylcarnitine analysis is performed for the biochemical detection of disorders of mitochondrial fatty acid β-oxidation and organic acid metabolism. The conditions revealed by acylcarnitine analysis have in common the accumulation of short, medium, and/or long-chain acyl-CoA species, which are substrates for one of several carnitine acyl-CoA transferases expressed in different intracellular compartments. Laboratories providing this analysis as a clinical service most often perform flow- injection analysis–tandem mass spectrometry (FIA-MS/MS) as the analytical platform. Recently MS/ MS methods which involve a liquid chromatographic (LC) separation step to quantitate acylcarnitine forms.