A separation method using high-performance capillary electrophoresis was applied to the analysis of calcium- and zinc-binding proteins. Calcium-binding proteins (calmodulin, parvalbumin, thermolysin and proteolytic peptides of calmodulin), zinc-binding proteins (carbonic anhydrase and thermolysin), and internal standard proteins (carbonic anhydrase and lactoglobulin) were separated completely by capillary electrophoresis. Calcium- and zinc-binding proteins were obtained under Ca2+ and Zn2+-containing conditions, respectively, cation-chelating conditions for the binding shift assay, and they showed that the binding shift depended on cations in the electrophoresis buffer in capillary zone electrophoresis and micellar electrokinetic chromatography. Two kinds of hydrophobic probes affected the electrophoretic mobility of calmodulin by interaction between its hydrophobic region and the hydrophobic probes under Ca2+-containing conditions.