Proteoglycans regulate diverse functions in the CNS by interacting with a number of growth factors, matrix proteins and cell surface molecules. Heparan sulfate and chondroitin sulfate are two major glycosaminoglycans present in the PGs of CNS. Functionality of these PGs is to a large extent dictated by the fine sulfation patterns present on their GAG chains. In the past 15 years, there has been a significant expansion in our knowledge on the role of HS and CS chains in various neurological processes such as neuronal growth, regeneration, plasticity and pathfinding. However, defining the relationship between distinct sulfation patterns of the GAGs and their functionality has so far been difficult. With the emergence of novel tools for synthesis of defined GAG structures, and techniques for their characterization, we are now in a better position to explore the structure—function relationship of GAGs in the context of their sulfation patterns. In this review, we discuss the importance GAGs on CNS development, injury and disorders with an emphasis on their sulfation patterns. Finally, we outline several GAG based therapeutic strategies to exploit GAG chains for ameliorating various CNS disorders.