The measurement of gamma-aminobutyric acid (GABA) and glutamic acid (Glu) in the whole brain and in various regions of the brain in 3-mercaptopropionic acid (3-MPA)-treated rats has been developed using liquid chromatography-mass spectrometry with an atmospheric pressure ionization interface system. The recoveries of these compounds were 94.90+/-4.18% for GABA, 95.60+/-2.86% for Glu after ion-exchange treatment. The detection limits for GABA and Glu were 2.5+/-0.3 microg/ml and 5.0+/-0.8 microg/ml, respectively, when 20 microl sample were injected. GABA concentration in the whole brain decreased gradually to 5 min and reached 63% of normal value after administration of 3-MPA, and the concentration increased gradually thereafter until 60 min. Conversely, the concentration of Glu in the whole brain increased gradually to 10 min and reached 154% of normal value, and after that decreased gradually and reached almost normal level at 60 min after administration of 3-MPA. GABA concentration in various regions of brain decreased to 5 min in all regions after administration of 3-MPA, and reached normal levels at 60 min as in the whole brain. This method was found to be useful for studies of metabolism of GABA and Glu in biological samples.