Fatty acid-binding protein (FABP) has been isolated from rat liver cytosol by two steps of gel-permeation chromatography on Sephadex G-75 and Sephacryl S-100 after ammonium sulfate precipitation. FABP fraction was eluted as two well-separated peaks, fractions A and B, by reversed-phase high-performance liquid chromatography (HPLC). The structural difference between the two fractions was investigated by lysyl endopeptidase digestion followed by reversed-phase HPLC of the digests, which identified a peptide corresponding to residues 58 through 78 as the modified peptide. Matrix-assisted laser-desorption-ionization mass spectrometry and other chemical analyses of the peptides established the modification in fraction A as cystein-thiolation at cysteine-69. This was confirmed by reduction and reoxidation of the peptide and the parent molecules. The modification did not affect binding of fluorescent derivatives of fatty acids. However, the modified species was more susceptible to proteolysis by bovine spleen cathepsin B and cathepsin D than the unmodified species. The presence of a relatively large amount of cysteine (but not of glutathione) mixed-disulfide form of FABP suggests some physiological role of this modification related to the redox status of the cell [Thomas, J.A., Poland, B., and Honzatko, R. (1995) Arch. Biochem. Biophys. 319, 1-9], and accounts, at least in part, for the extensive heterogeneity of liver FABP.