We describe a gas chromatographic/mass spectrometric method for the accurate determination of n-hexanoylglycine, 3-phenylpropionylglycine and suberylglycine in urine for the diagnosis of hereditary medium-chain acyl-CoA dehydrogenase (MCAD) deficiency. These acylglycines had previously been detected in urine from patients with MCAD deficiency, but their diagnostic values were unknown because of a lack of appropriate analytical methods. n-Hexanoyl(1,2-13C)glycine, 3-phenylpropionyl(2-13C,15N)glycine and suberyl(2-13C,15N)glycine were synthesized and used as internal standards. Ammonia chemical ionization was utilized to generate intense [M + H]+ ions for selected-ion monitoring quantification. The whole procedure is fast and can be performed by a low-resolution gas chromatographic/mass spectrometric system, giving accurate results over a range of three orders of magnitude (0.0167-16.7 micrograms/ml). The results from the analyses of 54 urine samples from 21 MCAD-deficient patients and various control samples using this method established that n-hexanoyglycine and 3-phenylpropionylglycine were highly diagnostic for this disease, while suberylglycine was found less specific.