Locations of pontomesencephalic cholinergic projection neurons from the laterodorsal tegmental (LDTg) and pedunculopontine tegmental (PPTg) nuclei to midbrain dopaminergic nuclei were mapped. Stereotaxic microinjections of Fluoro-Gold- or rhodamine-labeled microspheres were made either to substantia nigra (SN) or ventral tegmental area (VTA) in rat. Choline acetyltransferase was visualized immunohistochemically. Labeled cells were digitally mapped at multiple levels of the nuclei using an interactive computer/microscope system. SN-projecting neurons were distributed predominantly ipsilaterally in distinct regions of the PPTg: either at its rostral pole or caudally in an area ventromedial to the superior cerebellar peduncle. Few SN-projecting neurons were found in LDTg. VTA-projecting neurons were distributed bilaterally throughout the cholinergic group, primarily in the densest regions of the LDTg and caudal PPTg. Neurons were not strictly segregated into these patterns. Scattered cells belonging to either projection could be found throughout the cholinergic group on either side. Hierarchical log- linear analysis showed these differences in topographic distribution to be statistically significant. Subtraction of cell density images demonstrated well delineated regions of the cholinergic group where the projections were predominately either to SN or VTA. These data indicate a high degree of internal organization within the pontomesencephalic cholinergic group based on the location of efferent projections to SN or VTA. These findings support the concept that this cholinergic group is functionally organized in a manner which selectively innervates motor (SN) and limbic (VTA) dopaminergic nuclei.