The pattern of axonal regeneration, specificity of reinnervation, and terminal arborization in the brainstem by axotomized retinal ganglion cell axons was studied in rats with peripheral nerve grafts linking the retina with ipsilateral regions of the brainstem, including dorsal and lateral aspects of the diencephalon and lateral aspect of the superior colliculus. Four to 13 months later, regenerated retinal projections were traced using intraocular injection of cholera toxin B subunit. In approximately one-third of the animals, regenerated retinal axons extended into the brainstem for distances of up to 6 mm. Although axons followed different patterns of ingrowth depending on their site of entry to the brainstem, within the pretectum, they innervated preferentially the nucleus of the optic tract and the olivary pretectal nucleus in which they formed two types of terminal arbors. Within the superior colliculus, axons extended laterally and formed a different terminal arbor type within the stratum griseum superficiale. In the remaining two-thirds of the animals, retinal fibers formed a neuroma-like structure at the site of entry into the brainstem, or a few fibers extended for very short distances within the neighboring neuropil. These experiments suggest that regenerated retinal axons are capable of a highly selective reinnervation pattern within adult denervated retinorecipient nuclei in which they form well defined terminal arbors that may persist for long periods of time. In addition, these studies provide the anatomical correlate for our previous functional study on the re-establishment of the pupillary light reflex in this experimental paradigm.