Capillary zone electrophoresis (CZE) was used to separate the disaccharides produced by chondroitinase digestion of chondroitin sulfates. The main disaccharides formed upon depolymerization have identical charge and mass. Baseline resolution of these two compounds was achieved by selecting appropriate concentration and pH of a borate buffer. Validation of the method showed a good linearity of the response and a very satisfactory reproducibility of migration times with a relative standard deviation (RSD) of less than 0.4%. The reproducibility of peak areas was improved by using an internal standardization. The addition of cinnamic acid (internal standard) to the incubation medium allowed us to perform kinetic measurements of the depolymerization while keeping a baseline resolution of the two main disaccharides analyzed during the complete digestion course even when their concentration in the incubation medium increased. Application of this method to the comparison of the rate of hydrolysis of chondroitin sulfate and of a complex associating chondroitin sulfate with chitosan showed clearly that, at the physiological pH, chitosan protected the chondroitin sulfate from depolymerization. This phenomenon was more pronounced as the pH of the incubation medium was far from the optimum pH activity of the chondroitinase.