The performance of commercial and enzymatically modified size-exclusion (SE) gels in electrochromatography was compared for preparative protein separations. Dextran and agarose-based SE gels were subjected to enzymatic digestion under mild conditions. This treatment partially hydrolyzed the gel matrix modifying its pore size distribution. Enzymatic treatment of agarose-based SE gels was found to increase the resolution of the separation. Successful separation of preparative amounts of the A and B forms of beta-lactoglobulin (difference in electrophoretic mobility of 8.5%) was achieved with a high degree of purity using agarose-based SE gels. The four major whey proteins, beta-lactoglobulin, alpha-lactalbumin, BSA and immunoglobulins, were purified from an acid whey preparation. The degree of retention of a protein in electrochromatography followed their free-solution electrophoretic mobility (mu) when the protein was able to enter the gel pores and the ratio of diffusion/mu when the protein was excluded.