A new cystathionine metabolite has been identified in the urine of a patient with cystathioninuria using liquid chromatography-mass spectrometry with an atmospheric pressure chemical ionization interface system (LC/APCI-MS). By this method a very intense quasi-molecular ion was observed as a base peak of synthetic N-acetyl-S-(3-oxo-3-carboxy-n-propyl)cysteine (NAc-OCPC). The quasimolecular ion [M + H]+ of NAc-OCPC observed in the urine of a patient with cystathioninuria was the same as that of the authentic compound (m/z 264). The retention time and Rf value on paper chromatography of the synthetic compound were the same as those of the urinary compound from the patient with cystathioninuria. From these results, this new cystathionine metabolite was identified as N-acetyl-S-(3-oxo-3-carboxy-n-propyl)cysteine.