The interaction between omeprazole or pantoprazole and bovine serum albumin (BSA) has been investigated in the absence and presence of Cu(II) or Fe(III) by means of fluorescence spectroscopy. The fluorescence intensity of BSA decreased remarkably with slight blue shifts by adding omeprazole or pantoprazole. Similar blue shifts and fluorescence shape with larger quenching extent of BSA were observed with increasing concentrations of omeprazole or pantoprazole in the presence of Cu(II) or Fe(III). The presence of Cu(II) and Fe(III) increased the affinities of omeprazole with BSA about 12.0% and 3.9%, while the presence of Cu(II) decreased the affinity of pantoprazole with BSA about 25.7%, and the presence of Fe(III) improved the affinity of pantoprazole with BSA about 16.3%. The changeable affinity and increased binding distance in the presence of metal ions may result from a noncompetitive binding in different albumin sites. The results indicated that the structures of omeprazole or pantoprazole and kinds of metal ions together affected the binding interaction with BSA, which may have relevant consequence in rationalizing dosage for patients with gastric ulcer.