Perineuronal nets are lattice-like accumulations of extracellular matrix components around the cell body and perisomatic portion of certain neurons. Whereas interneurons associated to this specific neuron-associated sheath have been elaborately classified, less effort has been undertaken to describe the occurrence of perineuronal nets around pyramidal neurons. Our aim was to give a detailed and comparative description of the occurrence of net-associated pyramidal cells throughout the rat neocortex as well as to systematically and comparatively analyze the relation of main projection types of principal neurons to the presence of perineuronal nets. The present study revealed that perineuronal nets stained with WFA were associated rather rarely to pyramidal cells compared to interneurons in layers II/III and V/VI of rat neocortex. However, their frequency was considerably different between various cortical areas with a maximum in visual cortex and with a minimum in secondary motor cortices. Further analysis revealed that neuron-associated matrix sheaths around principal cells were more common in the primary than in the secondary fields of corresponding areas and they were more numerous in infra-than in supragranular layers in most regions. Subfields of cortical areas also differed regarding the occurrence of net-associated principal cells, and the subtlety of cortical representation seemed to correlate with the frequency of perineuronal nets around pyramidal neurons in the primary somatosensory cortex. It appears that net-associated pyramidal cells do not have a projection pattern restricted to distinct target regions. Rather a functional heterogeneity of the pyramidal cell population contributing to specific intra-or subcortical projections is suggested.