Crude membrane preparations of fungi contain the enzyme glucan synthase (EC 184.108.40.206) which produces a polymer of glucose linked through 1,3-beta-glycosidic bonds. This polymer is a major structural element of the fungal cell wall. Preparations of glucan synthase are contaminated with the enzyme glycogen synthase (EC 220.127.116.11). Glycogen synthase forms the storage carbohydrate glycogen, a polymer of glucose consisting of mainly 1,4-alpha-glycosidic linkage. Both enzymes utilize uridine diphosphoglucose as substrate. Discrimination of glucan synthase from glycogen synthase activity has relied upon the inclusion of glycogen-degrading enzymes in the crude reactions. The polysaccharide reaction products of glucan synthase assays have been characterized by their susceptibility to enzymatic degradation by various glucanohydrolases. These degradative enzymes are impure and inclusion of appropriate control polysaccharides often leads to ambiguous results. A method for comparative qualitative analysis of polysaccharides formed in fungal glucan synthase reactions has been developed using high-performance anion-exchange chromatography. Using this method, polymers of glucose with 1,3-beta-glycosidic linkage and 1,4-alpha linkage can be readily distinguished. This method has been applied to map oligosaccharides derived by partial acid hydrolysis from fungal glucan synthase reaction products from Candida albicans protoplasts prepared by two different methods.