Chondroitin sulfate proteoglycans (CSPGs), consisting of a core protein and the glycosaminoglycan chondroitin sulfate (CS) sugar chains, are the major components of the extracellular matrix (ECM). Perineuronal nets (PNNs), high-density complexes of ECM molecules, appear around a subset of neurons in the mature brain and CSPGs accumulate in PNNs. It is well known that the treatment of CS-degrading enzyme against the PNNs increases the neuronal plasticity, suggesting that CSPGs in PNNs are involved in the brain functional maturation. The glycan diversity of PNNs in various regions has not been characterized in spite of these approaches. We examined the mechanisms underlying glycan diversity of PNNs on this study. The glycan pattern of PNNs was divided into several types by histochemical studies using a CS-binding lectin (Wisteria Floribunda agglutinin; WFA) and the CS-recognizing antibody Cat315. We confirmed that these probes labeled PNNs differently in the distinct brain regions. We have already produced knockout (KO) mice lacking in the crucial CS-synthesizing enzymes CSGalNACT1 (T1) and CSGalNAcT2 (T2), and demonstrated that each of KO mice altered glycan pattern in PNNs, respectively. In T1-KO mice, WFA (+) PNNs remarkably decreased throughout the regions in the brain, while several parts of WFA (+) PNNs remained in the somatosensory cortex. Interestingly, wild type (WT) and T1 KO had PNNs with WFA (+) / Cat315 (-) and WFA (-) / Cat315 (+), respectively in this region. In T2-KO mice, although most of the PNNs appeared intact, decrease of WFA (+) PNNs in the somatosensory cortex was more evident than in T1-KO and in WT. In addition, the glycan patterns of PNNs in T2 KO were different from those of T1-KO in the somatosensory cortex of T2-KO, PNNs with WFA (+) / Cat315(+) shifted to those with WFA (-) / Cat315(+). Taken together, there results suggest that T1 and T2 are differentially involved in the regulation of glycan diversity in PNNs.