Chondroitin sulfate proteoglycans (CSPGs) consist of chondroitin sulfate (CS) glycosaminoglycans (GAGs) and core protein and regulate the migration, axonal outgrowth, and synaptogenesis in mammalian brains. In the present study, we investigated the localization of CSPGs, the effects of sensory deprivation on the density of perineuronal nets (PNNs), and the effects of chondroitinase ABC (Chase) on the formation of barrel structures in the posterior medial barrel subfield (PMBSF). In developing mouse and rat brains, the immunoreactivity of chondroitin-6-sulfate containing proteoglycan (CS-6-PG), phosphacan, and neurocan was stronger at barrel septa as compared with barrel hollows and surrounding cortex, while the labeling of Wisteria floribunda agglutinin (WFA) was observed at barrel hollows. In adult brains, CS-6-PG-immunoreactive and WFA-labeled PNNs were observed mainly at barrel hollows of mouse, but they were seen chiefly at barrel septa of rats. Sensory deprivation of facial vibrissae reduced the number of WFA-labeled PNNs at barrel hollows but not at barrel septa. Intracerebral injection of Chase did not affect the formation of barrel structures in the PMBSF. These data indicate species-dependent heterogeneity of CSPG expression and activity-dependent formation of PNNs in the PMBSF, but CS GAGs have no crucial function in constructing the barrel structures during early postnatal development.