The application of capillary electrophoresis to total compositional analysis of heparin and low-molecularweight heparin samples has been studied. Optimum resolution of 17 defined oligosaccharides was obtained with the buffer system composed of (10 \mathrm{~mm}) sodium borate and (50 \mathrm{~mm}) sodium dodecyl sulfate at (\mathrm{pH} 8.81) and at a constant voltage of (20 \mathrm{kV}). The ratio of oligosaccharide charge to the number of saccharide residues correlated with the migration time. For oligosaccharides having the same charge to saccharide ratio, the larger of the oligosaccharides eluted earlier. A hexasaccharide, having a 3- (O)-sulfated glucosamine residue at the reducing end and arising from heparin's antithrombin III binding site, migrated in an unusual fashion. The limit of oligosaccharide detection was from (600 \mathrm{fmol}) to 1 pmol. Quantitative analysis could conveniently be performed on (10 \mathrm{pmol}) of an oligosaccharide sample. Oligosaccharide composition using capillary electrophoresis was obtained by nearly complete depolymerization of heparins with a mixture of heparin lyase I, II, and III. The analysis resulted in (95 %) mass balance for both heparin and low-molecular-weight heparin. Capillary electropherograms of heparin and different low-molecularweight heparins depolymerized with heparin lyase I alone showed a high level of structural heterogeneity in the products formed. The oligosaccharide maps thus obtained might find use in fingerprinting the heparin and low-molecular-weight samples. O 1983 Academic Press, Inc.