Carbohydrates, in particular the complex carbohydrates conjugated to proteins and lipids, have important functions in a variety of biological systems. Their isolation and structural determination--prerequisites for elucidation of their biological functions--have been technical challenges for many decades. Almost all available chromatographic and electrophoretic methods as well as NMR and MS have been applied to carbohydrate analysis but none has proved satisfactory in terms of simplicity, sensitivity, reproducibility, cost and requirement for materials. Recently, a technique called fluorophore-assisted carbohydrate electrophoresis was developed which is very promising. It separates fluorescently-labeled carbohydrates on polyacrylamide gels and uses a charge-coupled device camera to detect and quantitate the products. This review describes the principles of the method and its applications to several aspects of research on carbohydrate-containing biological biomolecules.