We have examined the influence of free metal ions on the affinity of structurally-defined proteins and peptides for model surface-immobilized metal ions. The model proteins chosen differed widely in both the type and quantity of surface-accessible electron donor groups. Metal ion affinity chromatography and equilibrium binding analyses demonstrated that the presence of excess free Cu(II) ions did not measurably affect either the affinity or the binding capacity of lysozyme for immobilized iminodiacetate-Cu(II). Similarly, the presence of excess free Cu(II) ions did not detectably affect the chromatographic behavior or measured affinity of either copper-saturated lactoferrin or iron-saturated lactoferrin for the immobilized Cu(II) ions. Its binding capacity however, was diminished. The affinities of small peptides for immobilized Cu(II) ions was found to be related to their number of His residues. Peptides with 0, 1, 2 and 3 His residues were resolved by high-performance immobilized Cu(II) affinity chromatography in both the presence and absence of added Cu(II) ions. In the presence of excess free Cu(II) ions, however, retention (affinities) of these peptides by immobilized Cu(II) ions was increased in relation to their number of His residues. These data demonstrate that protein surface binding sites for free and immobilized metal ions are functionally distinct. The presence of free and/or protein surface-bound metal ions does not preclude interaction with the same immobilized metal ions. Stationary phase immobilized metal ions can be a useful model system through which we can better understand the influence of macromolecular surface-immobilized metal ions on macromolecular recognition events. The significance of these findings are also important to the design of other site-specific and domain-specific affinity reagents involving metal ions.