Carnitine is an endogenous quaternary amine whose primary function is to shuttle long chain fatty acids to the mitochondrial matrix, where they subsequently undergo beta oxidation. Accurate quantification of total and free carnitine is essential for the accurate diagnosis of a number of inborn errors of metabolism, including disorders of fatty acid oxidation as well as various organic acidurias. Early methods for carnitine measurement were enzyme based. Recently, liquid chromatography tandem mass spectrometry has become the method of choice for carnitine measurement. Typically, carnitine is derivitized to from a butyl ester, thus improving its ionization and retention characteristics. A potential problem with this approach is that the acidic conditions used to carry out the reaction may hydrolyze other acyl esters, resulting in ex-vivo artifacts. Consequently, we developed a hydrophobic interaction chromatography (HILIC) tandem mass spectrometry method for the quantification of carnitine. The use of HILIC allows for the derivitization step to be circumvented, while still allowing for favorable chromatographic performance. The method was shown to be accurate, precise, and robust.