The isolectin Vicia villosa B(4) (VV) selectively recognizes N-acetyl-galactosamine-terminal glycoconjugates that form perineuronal nets (PNNs) around a subset of neurons in the cerebral cortex. PNNs are thought to participate in the guidance of incoming thalamic axons and in the posterior stabilization and maintenance of synaptic contacts. Here we examine the spatial and temporal distribution of biotinylated VV in tangential sections through layer IV of the posteromedial barrel subfield in the primary somatosensory cortex (PMBSF) of rats ranging from postnatal day (P)3 to P60, which underwent unilateral deafferentation of whiskers at birth. In the afferented hemisphere, labeling first appears at P5, with a diffuse distribution, probably associated with neuropil, inside PMBSF barrels. VV distribution remains diffuse during the following week, and declines around P17. From P24 onward, however, proteoglycans form PNNs around cell bodies preferentially localized in septal regions of the PMBSF. In the contralateral, deafferented PMBSF the diffuse labeling also appears on P5, but first develops into elongated, homogeneous stripes, which disappear after P24, leaving only scattered cell bodies along layer IV. Our results indicate that proteoglycans appear simultaneous to barrel formation in the developing rat while segregation of PNNs to septal cells might be driven by afferent activity.