In the central nervous system (CNS) chondroitin sulfate proteoglycans, as one of the major barrier-forming molecules, influence cell migration patterns and axon pathfinding. By contrast, chondroitin sulfate side chains often form hybrid chains with dermatan sulfate and serve as a neural stem cell marker and neurogenic/neuritogenic molecules involved in neural stem cell proliferation. Hybrid chondroitin/dermatan sulfate chains are also involved in formation of the neural network by capturing and presenting heparin-binding growth factors like basic fibroblast growth factor, pleiotrophin, and hepatocyte growth factor to stem cells or neuronal cells. Research tools for structural glycobiology are emerging to perform a high-throughput screening of glycosaminoglycans for the binding to ligands, to decipher sulfation patterns of rare functional oligosaccharide sequences and to build structural models for the shape of such sulfated oligosaccharides.