Capillary electrophoresis based on cetyltrimethylammonium bromide micellar electrokinetic capillary chromatography (MECC) was developed for the separation and determination of glycosaminoglycan (GAG) disaccharide units without derivatization. The influence of changes in several separation conditions was studied, and the separation mechanisms are discussed. Tests of repeatability and linearity were performed for qualitative and quantitative evaluation of the method. The described procedure gives a rapid and efficient determination of GAG disaccharides. Samples of chondroitin sulphates and mink skin were treated with proteases, and the extent of protein cleavage was followed by free zone capillary electrophoresis. The result of the chondroitinase ABC treatment following the protease treatment was evaluated by the MECC method.