The retrograde transport of the conjugate wheat germ agglutinin-horseradish peroxidase (WGA-HRP) was used in the rat to identify the cell bodies of origin for all subcortical projections to the basilar pontine nuclei (BPN). A parapharyngeal surgical approach was used to allow the injection micropipette to enter the BPN from the ventral aspect of the brainstem and thus avoid any potential for false-positive labeling due to transection and injury-filling of axonal systems located dorsal to the basilar pontine gray. A surprisingly large number of BPN afferent cell groups were identified in the present study. Included were labeled somata in the lumbar spinal cord and a large variety of nuclei in the medulla, pons, and midbrain, as well as labeled cells in diencephalic and telencephalic nuclei such as the zona incerta, ventral lateral geniculate, hypothalamus, amygdala, nucleus basalis of Meynert, and the horizontal nucleus of the diagonal band of Broca. Quite a number of cell groups known to project directly to the cerebellum also exhibited labeled somata in the present study. To explore the possibility that such neurons were labeled because their axons were transected and injury-filled as they coursed through the BPN injection site to enter the cerebellum via the brachium pontis, a series of rats received complete, bilateral lesions of the brachium pontis followed 30-60 minutes later with multiple, diffuse injections of WGA-HRP (12-16 placements per animal) throughout the cerebellar cortex. In another series of animals, the massive cerebellar WGA-HRP injections were not preceded by brachium pontis lesions. In the latter cases, each of the cell groups in question that were known to project directly to the cerebellum exhibited labeled somata. However, when the cerebellar HRP injections were preceded by brachium pontis lesions, each of the cell groups in question continued to exhibit labeled somata in numbers comparable to that observed in the nonlesion cases. This implies that such neurons project to the BPN and the cerebellar cortex and that the axons of these particular neurons do not project to the cerebellum via the brachium pontis.