Using gas chromatography-mass spectrometry (GC/MS), urinary organic acid profile studies were carried out on a patient with dihydrolipoyl dehydrogenase (E3) deficiency. Elevated levels of 2-hydroxyglutaric acid, 2-hydroxyisocaproic acid and 2-oxoisocaproic acid were observed in addition to lactic acid, 2-oxoglutaric acid, 2-hydroxyisovaleric acid and 2-hydroxybutyric acid previously described in patients with E3 deficiency. The 2-oxoglutaric acid levels were significantly lowered after branched-chain amino acid restriction. In an acute period, the patient was slightly ketoacidotic and excreted larger amounts of 2-oxoglutaric acid and lactic acid than in a static period. It was shown that, prior to confirmatory enzyme studies, patients with E3 deficiency who were suspected to have atypical maple syrup urine disease or chronic lactic acidosis can be rapidly identified by GC/MS analysis of urinary acids.