Heparan sulfate (HS) and heparan sulfate proteoglycans (HSPGs) play significant roles in various biological processes. There is a wealth of circumstantial and experimental evidence suggesting the roles of HS in mammalian neural development. HS synthesis is governed by a series of enzymes. Among them, two enzymes, EXT1 and EXT2, catalyze polymerization of glucuronic acid and N-acetylglucosamine, the crucial step of HS synthesis. To obtain insight into the roles of HS in neural development, we examined the spatiotemporal expression patterns of EXT1 and EXT2 during mice brain development. RT-PCR analyses showed that expression of EXT1 and EXT2 peaks during early postnatal period in the cerebrum and around birth in the cerebellum. In situ hybridization revealed that in the embryonic brain, EXT1 and EXT2 were localized primarily in the neuroepithelial cells surrounding the lateral ventricles, the mesencephalic vesicle, and the fourth ventricle. In the early postnatal stage, intense expression of EXT1 and EXT2 was observed in the cerebral cortex and the hippocampus formation. In the postnatal cerebellum, expression of EXT1 and EXT2 was mainly observed in external and internal granular layers. Our results demonstrate that EXT1 and EXT2 are highly expressed in the developing brain, and that their expression is developmentally regulated, suggesting that HS is involved in various neurodevelopmental processes.