The topographical distribution of cholinergic cell bodies has been studied in the rat brain and spinal cord by choline acetyltransferase (ChAT)-immunohistochemistry and acetylcholinesterase (AChE)-pharmacohistochemistry using diisopropylfluorophosphate (DFP). The ChAT-containing cells and the cells that stained intensely for AChE 4-8 hr after DFP were mapped in detail on an atlas of the forebrain (telencephalon, diencephalon) hindbrain (mesencephalon, rhombencephalon) and cervical cord (C2, C6). Striking similarities were observed between ChAT-positive cells and neuronal soma that stained intensely for AChE both in terms of cytoarchitectural characteristics, and with respect to the distribution of the labelled cells in many areas of the central nervous system (CNS). In the forebrain these areas include the caudatoputamen, nucleus accumbens, medial septum, nucleus of the diagonal band, magnocellular preoptic nucleus and nucleus basalis magnocellularis. In contrast, a marked discrepancy was observed in the hypothalamus and ventral thalamus where there were many neurons that stained intensely for AChE, but where there was an absence of ChAT-positive cells. No cholinergic perikarya were detected in the cerebral cortex, hippocampus, amygdala and dorsal diencephalon by either histochemical procedure. In the hindbrain, all the motoneurons constituting the well-established cranial nerve nuclei (III-VII, IX-XII) contained ChAT and exhibited intense staining for AChE. Further, a close correspondence was observed in the distribution of labeled neurons obtained by the two histochemical procedures in the midbrain and pontine tegmentum, including the laterodorsal tegmental nucleus, some areas in the caudal pontine and bulbar reticular formation, and the central gray of the closed medulla oblongata. On the other hand, AChE-intense cells were found in the nucleus raphe magnus, ventral part of gigantocellular reticular nucleus, and flocculus of the cerebellum, where ChAT-positive cells were rarely observed. According to both techniques, no positive cells were seen in the cerebellar nuclei, the pontine nuclei, or the nucleus reticularis tegmenti pontis. Large ventral horn motoneurons and, occasionally, cells in the intermediomedial zone of the cervical cord displayed ChAT-immunoreactivity and intense AChE staining. On the other hand, AChE-intense cells were detected in the dorsal portion of the lateral funiculus, but immunoreactive cells were not found in any portion of the spinal cord white matter.(ABSTRACT TRUNCATED AT 400 WORDS)