In primary sensory and motor cortex of adult animals, alteration of input from the periphery leads to changes in cortical topography. These changes can be attributed to processes that are intrinsic to the cortex, or can be inherited from alterations occurring at stages of sensory processing that are antecedent to the primary sensory cortical areas. In the visual system, focal binocular retinal lesions initially silence an area of cortex that represents the region of retina destroyed, but over a period of months this area recovers visually driven activity. The retinotopic map in the recovered area is altered, shifting its representation to the portion of retina immediately surrounding the lesion. This effectively shrinks the representation of the lesioned area of retina, and expands the representation of the lesion surround. To determine the loci along the visual pathway at which the reorganization takes place, we compared the course of topographic alterations in the primary visual cortex and dorsal lateral geniculate nucleus (LGN) of cats and monkeys. At a time when the cortical reorganization is complete, the silent area of LGN persists, indicating that changes in cortical topography are due to alterations that are intrinsic to the cortex. To explore the participation of thalamocortical afferents in the reorganization, we injected a series of retrogradely transported fluorescent tracers into reorganized and surrounding cortex of each animal. Our results show that the thalamocortical arbors do not extend beyond their normal lateral territory and that this physical dimension is insufficient to account for the reorganization. We suggest that the long-range intrinsic horizontal connections are a likely source of visual input into the reorganized cortical area.