In recent years, the importance of glycosylation has been realized. Carbohydrates not only serve as decoration for proteins and lipids but also form an integral part of the glycoconjugate, adding to its functional and structural properties. The specific type of glycosylation may change with altering physiological conditions, such as disease. Likewise, altering glycosylation may determine disease or disease properties. Studying glycosylation has long been a major problem, mainly because of the lack of proper analytical technology. Only minute quantities of the analytes are available from natural sources, and they cannot be amplified like DNA. The possibility of branching, different isomeric linkages, and the use of building blocks with the same mass lead to isomeric and isobaric structures. Lately, technology has become available that is able to differentiate these structures and that comforts enough sensibility and throughput to analyze samples from natural sources. DNA sequencer-aided fluorophore-assisted carbohydrate electrophoresis (DSA-FACE) is one of these new techniques with great potential. Here, we briefly introduce the method and discuss some of its applications in diagnosis of disease.