The enzyme xanthine oxidase (XOD) has an affinity for heparin and can bind to cultured porcine aortic endothelial cells. We have reported that the exposure of human XOD (h-XOD) to the lysine-specific reagent trinitrobenzenesulfonic acid or the arginine-specific reagent phenylglyoxal caused it to lose its affinity for heparin-Sepharose. The heparin-binding sites in h-XOD are further studied in the present article. From a chymotryptic digest of cyanogen bromide fragmented h-XOD, two peptides with an affinity for heparin-HPLC, A-1 and A-2, were isolated. Amino acid sequence analysis showed that both peptides had lysine and/or arginine residues. The A-1 region may direct its charged side chains toward the solvent while burying its hydrophobic side chains against the hydrophobic inside, because the A-1 peptide forms a highly amphipathic structure. Peptide A-2 contains triple lysine residues and constitutes a hydrophilic region.