We have developed techniques for the separation of unsulfated (2-acetamido-2-deoxy-3-O-(4-deoxy-α-l-threo-hex-4-enopyranosyluronicacid)-d-galactose and -d-glucose), monosulfated (2-acetamido-2-deoxy-3-O-(4-deoxy-2-O-sulfo-α-l-threo-hex-4-enopyranosyluronic acid)-d-galactose and 2-acetamido-2-deoxy-3-O-(4-deoxy-α-l-threo-hex-4-enopyranosyluronic acid)-4-sulfo-d-galactose and -6-sulfo-d-galactose), disulfated (2-acetamido-2-deoxy-3-O-(4-deoxy-2-O-sulfo-α-l-threo-hex-4-enopyranosyluronic acid)-4-sulfo-d-galactose and -6-sulfo-d-galactose and 2-acet-amido-2-deoxy-3-O-(4-deoxy-α-l-threo-hex-4-enopy-ranosyluronic acid)-4,6-di-O-sulfo-d-galactose), and trisulfated (2-acetamido-2-deoxy-3-O-(4-deoxy-2-O-sulfo-α-l-threo-hex-4-enopyranosyluronic acid)-4,6-di-O-sulfo-d-galactose) isomers of chondroitin using capillary zone electrophoresis. In addition, it is possible to separate oligomers of hyaluronan by similar protocols. These techniques represent a rapid, sensitive, and reproducible technique for the assay of these molecules from digests of connective tissues. © 1991.