The intranuclear organization of divergently projecting neurons of the midbrain raphe in the rat was studied by using double retrograde axonal tracing. Paired injections of the tracers N-[acetyl-3H] WGA and horseradish peroxidase were made within known projection targets of the midbrain raphe (caudate-putamen, amygdala, hippocampus, substantia nigra, and locus coeruleus). After injections of either tracer in the aforementioned targets, retrograde labeled neurons were found mainly ipsilaterally and within midline portions of the dorsal raphe nucleus, its caudal B6 portion, and within the linear and superior central nuclei of the median raphe complex. There are discrete intranuclear distributions of raphe neurons that project to these forebrain and brainstem sites, and there is an overall rostrocaudal topographic order within the raphe with neurons projecting to the neostriatum, amygdala, and substantia nigra residing most rostrally and neurons projecting to the hippocampus and/or locus coeruleus occupying caudal portions of the B6 and superior central nuclei. Such distributions of projection neurons suggest the existence of an "encephalotopic" intranuclear organization within the raphe; that is, each central nervous system structure that receives midbrain raphe projections has its own unique representation within a topographically distinct portion of one or more of the raphe subgroups. These findings suggest an overall functional organization within the midbrain raphe nuclear complex whereby rostral portions are associated with the basal ganglia and related nuclei, and caudal portions relate to the limbic system. An intermediate representation of amygdala-projecting raphe neurons functionally conjoins the two. Collateralized neurons are found within complex zones of overlap in the topographically organized distributions of raphe neurons projecting to functionally related structures.