Medium-chain acyl-CoA dehydrogenase (MCAD) deficiency, one of the most common inherited metabolic disorders, is often mistaken for the sudden infant death syndrome or Reye's syndrome. Diagnosing it has been difficult because of a lack of fast and reliable diagnostic methods. We developed a stable-isotope dilution method to measure urinary n-hexanoylglycine, 3-phenylpropionylglycine, and suberylglycine, and we retrospectively tested its accuracy in diagnosing MCAD deficiency. We measured the concentrations of these three acylglycines in 54 urine samples from 21 patients with confirmed MCAD deficiency during the acute and asymptomatic phases of the illness and compared the results with the concentrations in 98 samples from healthy controls and patient controls with various diseases. The levels of urinary hexanoylglycine and phenylpropionylglycine were significantly increased in all samples from the patients with MCAD deficiency, clearly distinguishing them from both groups of controls. Although urinary suberylglycine was increased in the patients, the range of values in the normal controls who were receiving formula containing medium-chain triglycerides was very wide, overlapping somewhat with the values in the patients with asymptomatic MCAD deficiency. These results indicate that the measurement of urinary hexanoylglycine and phenylpropionylglycine by our method is highly specific for the diagnosis of MCAD deficiency. The method is fast and can be applied to random urine specimens, without any pretreatment of patients.