The dependence of amino acids fluxes through the ion-exchange membranes during electrodialysis on the current density was studied. It is found that this dependence is maximum at limiting current density. The decrease of amino acid fluxes, glycine as an example, explains the barrier effect of polarized boundary layers near the membranes in the solution of desalting compartment. The barrier effect makes it possible to effectively separate amino acids and mineral components. The role of this effect during the separation of amino acids mixtures (tyrosine-histidine) is also considered.