An HPCE method is described for the determination of disaccharides present in chondroitin sulfate/dermatan sulfate of different origins. Following chondroitinase digestion, nonsulfated, monosulfated and disulfated Delta-disaccharides, are separated and readily determined within 60 min on an uncoated fused-silica capillary using normal polarity at 20 kV and detection at 230 nm. Comparison was made by separation of these disaccharides in strong-anion exchange-HPLC. The system was applied to the analysis of chondroitin sulfate samples obtained from bovine, porcine and chicken tracheas, from shark cartilage, and of dermatan sulfate from porcine skin. The results indicate the existence of particular electropherographic as well as chromatographic patterns for each sample in the study, with some similitudes and differences.