The lateral septum (LS) plays a role in the adjustment of behavioral responses according to environmental demands. This is a complex integrative process wherein a variety of modulatory systems, i.e. cholinergic, dopaminergic and serotonergic projections forming pericellular baskets around LS neurons, are involved. Recently, vesicular glutamate transporter 3 (VGLUT3)-immunoreactive (-ir) structures outlining unlabeled somata and their proximal dendrites were described in the LS. However, the vesicular transporters for acetylcholine and GABA were not or only rarely co-expressed with VGLUT3. In this study, the morphology and distribution of these VGLUT3-ir structures were systematically analyzed revealing that (1) they form distinct pericellular baskets (PBs) displaying variable shapes, (2) they are arranged in a layer-like pattern similar to the terminals of other modulatory systems, (3) beside a few exceptions (e.g., choline acetyltransferase), they are generally not or very sparsely co-localized with other neurochemical markers characterizing major neuron populations or afferent systems of the LS, i.e. calcium-binding proteins, tyrosine hydroxylase, tryptophan hydroxylase, vesicular glutamate transporters 1 (VGLUT1) and 2 (VGLUT2) and the vesicular GABA transporter. Thus, in the LS, a separate population of neurons is covered by VGLUT3-ir PBs. The distribution pattern and the lack of co-localization indicate that the VGLUT3-expressing cells of origin are located in the brainstem and that they could be pure glutamatergic projection neurons-different from the well-defined canonical VGLUT1- and VGLUT2-expressing neurons. Alternatively, they could simultaneously express VGLUT3 and second transmitter, but use different release sites inside the LS for both.