A comparative study on compositional analysis of two sets of eight unsaturated disaccharide standards derived from heparin/heparan sulfate and chondroitin/dermatan sulfate was carried out using capillary electrophoresis performed in both normal and reverse polarity modes. While these heparin/heparan sulfate disaccharides (S. A. Ampofo, H. M. Wang, and R. J. Linhardt (1991) Anal. Biochem. 199, 249-255) and chondroitin/dermatan sulfate disaccharides (A. Al-Hakim and R. J. Linhardt (1991) Anal. Biochem. 195, 68-73) have previously been fractionated using normal polarity capillary electrophoresis, multiple buffer systems and conditions were required to separate certain disaccharide isomers and these separations often resulted in poor peak symmetry and significant tailing. This paper demonstrates that reverse polarity capillary electrophoresis completely resolves disaccharide mixtures into all components using a single buffer, 20 mM phosphoric acid-sodium phosphate at pH 3.48. This improved resolution is due primarily to an increase in the sharpness of peaks and improved peak symmetry. Separation of heparin-derived oligosaccharides, ranging from disaccharide to hexasaccharide, had also previously been reported using normal polarity capillary electrophoresis (U.R. Desai, H.M. Wang, S.A. Ampofo, and R.J. Linhardt (1993) Anal. Biochem. 213, 120-127). This paper now demonstrates the separation of 13 heparin-derived oligosaccharides of sizes ranging from disaccharide to tetradecasaccharide using both reverse and normal polarities. An enzymatic digestion of bovine lung heparin containing many of these larger oligosaccharides was also compared in both normal and reverse polarity modes. Mixtures containing oligosaccharides primarily differing in size (number of saccharide units) were better resolved using normal polarity.