Exogenous administration of chondroitin sulfate (CS) is widely practiced for the treatment of osteoarthritis, although the efficacy of this treatment has not been completely established by clinical studies. A reason for the inconsistency of the results may be the quality of the CS preparations, which are commercially available as dietary supplements. In this article, we describe the development of a new method of capillary electrophoresis (CE) for the quantification of CS concentrations, screening for other glycosaminoglycan or DNA impurities and determination of hyaluronan impurities in CS raw materials, tablets, hard capsules, and liquid formulations. Analysis is performed within 12 min in bare fused silica capillaries using reversed polarity and an operating phosphate buffer of low pH. The method has high sensitivity (lower limit of quantitation [LLOQ] values of 30.0 microg/ml for CS and 5.0 microg/ml for hyaluronan), high precision, and accuracy. Analysis of 11 commercially available products showed the presence of hyaluronan impurities in most of them (up to 1.5%). CE analysis of the samples after treatment with chondroitinase ABC and ACII, which depolymerize the chains to unsaturated disaccharides, with a previously described method (Karamanos et al., J. Chromatogr. A 696 (1995) 295-305) confirmed the results of hyaluronan determination and showed that the structural characteristics (i.e., disaccharide composition) of CS are very different, showing the different species or tissue origin and possibly affecting the therapeutic outcome.