Previous reports from this laboratory and elsewhere have provided evidence that the locus coeruleus (LC) and dorsal raphe (DR) nuclei are topographically organized with respect to their efferent targets. Whereas most of these previous studies have focused on relationships between these monoamine-containing brainstem nuclei and cerebral cortex, basal ganglia, and limbic structures, they have not systematically examined the distribution of LC and DR cells that project to multiple structures with common sensory or motor functions. The goal of the present study was to characterize and compare the distributions of LC and DR cells which project to different visual areas of the rat central nervous system. Long-Evans hooded rats received unilateral pressure injections of the retrograde tracer wheat germ agglutinin-horseradish peroxidase in either the dorsal lateral geniculate, ventral lateral geniculate, or lateral posterior nucleus of thalamus; superior colliculus, cortical area 17, cortical area 18a/b; cerebellar vermis (lobules VI and VII); or paraflocculus. Transverse sections through the midbrain and pons were examined by light microscopy after performing routine tetramethyl benzidine histochemical procedures. For all cases studied, retrogradely labeled cells were observed throughout the rostrocaudal extent of the LC and DR; however, labeling patterns which were distinctive for different injection sites were noted in each of these brainstem nuclei. The major conclusion drawn from this work is that subsets of LC and DR cells which project to different target structures within the rat visual system are found in overlapping but not necessarily coextensive zones within these nuclei. These studies provide further evidence of a rough topographic ordering within both the LC and DR nuclei, as well as support a new hypothesis that the outputs from each of these nuclei are organized with respect to the sensory related functions of their efferent targets.