The morphology, ultrastructure and synaptic relationships of the cholinergic and non-cholinergic neurons in the medial septal nucleus (MS) and vertical limb of the diagonal band of Broca (VDB) in the basal forebrain of the rat were studied at the light and electron microscopic levels. The cholinergic neurons were localized immunocytochemically using a monoclonal antibody against choline acetyltransferase (ChAT). Morphometric and statistical analyses showed that ChAT-labelled cells presented a predominantly oval morphology in both nuclei. The sizes of the neurons were significantly larger in the VDB nucleus. Within the two nuclei, two populations of cholinergic neurons were differentiated. One of the large immunolabelled neurons presented deep indentations and prominent nucleoli in their non-immunoreactive nuclei. Their cytoplasm contained a well-organized endomembrane system composed of short cisternae of rough endoplasmic reticulum (RER). One or two lamellar bodies with a peculiar ultrastructure were frequently found intercalated in this system. The Golgi areas presented numerous coated vesicles, sequestration and multivesicular bodies, which was indicative of an intense metabolic activity in these cells. The second population of small immunolabelled neurons exhibited reduced cytoplasm with a poorly developed endomembrane system and apparent absence of lamellar bodies. The neighbouring non-immunolabelled neurons presented a different type of organization of the endomembrane system which was composed of scattered and loosely arranged elongated cisternae of RER and infrequent lamellar bodies, with a structure different from that seen in the large cholinergic neurons. We propose that the structural differences in composition of the endomembrane system and lamellar bodies observed in the three types of neurons in this study indicate different metabolic activities. Symmetrical and asymmetrical synaptic contacts were observed on somata and dendrites of labelled neurons, the latter being more frequent. ChAT-labelled axon boutons were never seen. The absence of immunolabelled axon terminals and the presence of immunolabelled myelinated axons leads us to suggest that the majority of neurons in these areas are of the long projecting type.