Extracellular matrix proteoglycans, particularly those accumulated in perineuronal nets (PNs), have been shown to form characteristic distribution patterns in cortical and subcortical regions of adult mammals. Their involvement in sustaining mechanisms that are especially related to fast activities of neurons has been discussed as one of the possible functions. The present study deals with the spatial organization of extracellular matrix proteoglycans in brain stem regions that contain aminergic neurons, such as substantia nigra, ventral tegmental area (VTA), raphe nuclei and locus coeruleus (LC). As these nuclei are known to influence brain activity by modulatory functions exerting patterns of slow electric activity, it could be expected that PNs would be absent around aminergic cells. The staining of PNs with Wisteria floribunda agglutinin (WFA) was combined with the detection of catecholaminergic neurons by tyrosine hydroxylase immunoreactivity and of serotonergic neurons by tryptophan hydroxylase (TH) immunoreactivity using double fluorescence microscopy. It was found that the catecholaminergic and serotonergic neurons in the nuclear accumulations, as well as those scattered in adjacent regions, were not ensheathed by PNs. In contrast, several non-aminergic neurons intermingled with aminergic neurons in the raphe nuclei, in the substantia nigra pars compacta (SNC) and in the VTA, as well as many cells in the reticular part of the substantia nigra, were found to be surrounded by PNs. It can be concluded from these results that the absence of PNs around aminergic brain stem neurons, also previously shown for cholinergic basal forebrain neurons, appears as a characteristic feature common to cells that exert slow modulatory functions.