AbstractGlycosaminoglycans are a family of polydisperse, highly sulfated complex mixtures of linear polysaccharides that are involved in many life processes. Defining the structure of glycosaminoglycans is an important factor in elucidating their structure–activity relationship. Capillary electrophoresis has emerged as a highly promising technique consuming an extremely small amount of sample and capable of rapid, high‐resolution separation, characterization and quantitation of analytes. Numerous capillary electrophoresis methods for analysis of intact glycosaminoglycans and glycosaminoglycan‐derived oligosaccharides have been developed. These methods allow for both qualitative and quantitative analysis with a high level of sensitivity. This review is concerned with separation methods of capillary electrophoresis, detection methods and applications to several aspects of research into glycosaminoglycans and glycosaminoglycan‐derived oligosaccharides. The importance of capillary electrophoresis in biological and pharmaceutical samples in glycobiology and carbohydrate biochemistry and its possible applications in disease diagnosis and monitoring chemical synthesis are described. Copyright © 2002 John Wiley & Sons, Ltd.