The extracellular matrix of the central nervous system (CNS) serves as both a supporting structure for cells and a rich source of signaling molecules that can influence cell proliferation, survival, migration and differentiation. A large proportion of this matrix is composed of proteoglycans--proteins with long chains of polysaccharides, called glycosaminoglycans (GAGs), covalently attached. Although many of the activities of proteoglycans depend on their core proteins, GAGs themselves can influence cell signaling. Here we review accumulating evidence that two GAGs, chondroitin sulfate and hyaluronan, play essential roles during nervous system development but also accumulate in chronic CNS lesions and inhibit axonal regeneration and remyelination, making them significant hindrances to CNS repair. We propose that the balance between the synthesis and degradation of these molecules dictates, in part, how regeneration and recovery from CNS damage occurs.