Capillary affinity electrophoresis (CAE) has been employed to investigate quantitatively the interactions of valinomycin, macrocyclic depsipeptide antibiotic ionophore, with univalent cations, ammonium and alkali metal ions, K+, Cs+, Na+, and Li+, in methanol. The study involved measuring the change in effective electrophoretic mobility of valinomycin while the cation concentrations in the BGE were increased. The corresponding apparent stability (binding) constants of the valinomycin-univalent cation complexes were obtained from the dependence of valinomycin effective mobility on the cation concentration in BGE using a nonlinear regression analysis. The calculated apparent stability constants of the above-mentioned complexes show the substantially higher selectivity of valinomycin for K+ and Cs+ ions over Li+, Na+, and NH4+ ions. CAE proved to be a suitable method for the investigation of both weak and strong interactions of valinomycin with small ions.