The HNK-1 carbohydrate epitope, a sulfated glucuronic acid at the non-reducing terminus of glycans, is expressed on glycoproteins and glycolipids and modulates neurite outgrowth and synaptic plasticity by affecting the adhesive and anti-adhesive properties. It is known that the HNK-1 carbohydrate is synthesized through two key enzymes, glucuronyltransferases (GlcAT-P and GlcAT-S). In the present study, we investigated the localization of GlcAT transcripts and HNK-1 carbohydrate in the adult mouse brain with or without GlcAT-P gene using in situ hybridization histochemistry and immunohistochemistry. Region-specific expression patterns of both GlcAT transcripts were observed. Strong expression of GlcAT-P and moderate expression of GlcAT-S were seen in neuronal cells of several nuclei of limbic-related regions and of the sensory system and the cerebellum. It was shown histologically that the localization of HNK-1 carbohydrate paralleled the pattern of expression of GlcAT transcripts in the brain. Additionally, the localization of HNK-1 carbohydrate was restricted partially in the brain of GlcAT-P-deficient mice, while the HNK-1 carbohydrate was widely distributed over most of the brain of wild-type mice. The present study provides a new framework for understanding the network constructed by the HNK-1 carbohydrate in the central nervous system.