Glycosaminoglycans (GAGs) are non branched polysaccharides which are raising a great interest among the scientists for their biological roles. In fact GAGs play a pivotal role in several biological events, since they participate in and regulate cell adhesion, migration and proliferation. The quantification and analysis of the fine structure of GAGs are increasingly important not only for understanding many biological processes, but also for elucidate many critical aspects in human pathology development. Chondroitin sulfate (CS), heparan sulfate (HS) and keratan sulfate (KS) are commonly described as sulfated GAGs and these molecules are linked to a core protein forming proteoglycans; the sulfation pattern shows a high level of complexity and it is associated with specific function in the tissues. The only GAG without protein core is hyaluronan (HA), which is produced in almost all tissues, often with a molecular weight of 106 Daltons. Several human tissues contain high amount of GAGs and the change of the quantity and the structure of these macromolecules are described in tissue development and it is commonly associated with diseases. Electrophoretic methods based on the gel separation of 2-aminoacridone labelled HA and CS sulfate Δ-disaccharides, derived from GAG digestion with specific eliminases, have been recently proposed. These new techniques represent a suitable method for GAG fast and sensitive analysis. In this review we will describe the recently achieved methods on the GAG analysis based on the electrophoretic approach in comparison with the more standard chromatographic techniques (HPLC).