A method of gel electrophoresis which separates polydisperse acidic mucopolysaccharides (AMPS) solely on the basis of differences in charge density is described. The standard procedure is to use a 0.6% agarose gel at pH 3.0 in the E-C 470 apparatus. The method shows that AMPS with the same basic polysaccharide chain structure, extracted from different tissues, may differ in electrophoretic mobility. It resolves heparin from pig intestinal mucosa into 2 major components.