Total homocysteine, total cysteine, and methionine have been extracted and partially purified from serum and urine using reduction with 2-mercaptoethanol followed by cation-exchange chromatography and anion-exchange chromatography. The t-butyldimethylsilyl derivatives were prepared and analyzed using capillary gas chromatography-mass spectrometry with selected ion monitoring. The addition of DL-[3,3,3',3',4,4,4',4'-2H8]homocystine, DL-[3,3,3',3'-2H4]cystine, and L-[methyl-2H3]methionine to the starting samples prior to the reduction of all disulfides, including the deuterated internal standards, with 2-mercaptoethanol makes it possible to quantitate all three amino acids. Normal ranges for total homocysteine, total cysteine, and methionine have been determined in human and rat serum and in human urine.