Medium chain acyl-CoA dehydrogenase (MCAD) deficiency is an inborn error of fatty acid metabolism, which is difficult to diagnose, partly because of its unpredictable clinical presentation. A specific diagnostic marker is an increased excretion of certain medium chain acyl glycines. A sensitive and specific method has been developed for the extraction, derivatization, identification and quantitation of urinary medium chain acyl glycines by gas chromatography-negative ion chemical ionization mass spectrometry (GC-NICIMS). The following series of standard acyl glycines has been synthesized and characterized: hexanoyl, octanoyl, 3-phenylpropionyl and suberyl and their respective isotopomers (using 13C2-glycine; for use as internal standards). The range of excretion of these compounds in normal subjects has been established using this method and increased excretion of acyl glycines, particularly hexanoyl, 3-phenylpropionyl and suberyl was successfully demonstrated in three MCAD deficient subjects from one family.