In this study we have developed a capillary zone electrophoresis (CZE) method for the determination of the degree of deacetylation (DDA) of chitosan. The electrophoretic mobilities of chitosans were measured by using the optimized CZE conditions. An internal standard, hexammine cobalt(III) chloride, was used to improve the precision of the electrophoretic mobility measurement. We have constructed a linear calibration curve between the CZE measured mobilities and the 1H NMR determined DDAs ranging from 55.3% to 96.2%. Based on the established linear calibration equation and the CZE measured mobilities, we were able to obtain not only the average DDA values but also the DDA distribution profiles of the chitosan samples. Without prior sample treatment or purification, we have successfully employed the newly developed CZE method to characterize the reacetylation derivatives of chitosans and to detect the DDA variability in different lots of chitosan products.