Freezing injury to the cortical plate at postnatal day (P) 1 initiates a cascade of events that ultimately result in a focal neocortical malformation resembling human 4-layered microgyria. This malformation has been associated with widespread changes in neocortical and thalamic architecture and physiology. It was hypothesized that at least some of these alterations could result from connectional reorganization following early injury. The current experiment was designed to delineate the efferent and afferent connections between the cerebral hemispheres and between the cortex and thalamus of rats with induced cerebrocortical microgyria. Microgyria were induced in the parietal cortex of rats by freezing injury on postnatal day 1. In adulthood, injections of biotinylated dextran amine were made either in the microgyric cortex, in homologous regions of the opposite hemisphere, or in ipsilateral ventrobasal complex of the thalamus. Appropriately directed connections to homotopic areas were seen in some but not all microgyric rats. In addition, heterotopic projections to frontal and secondary sensorimotor cortices were noted. Projections from homotopic regions in the hemisphere opposite to the malformation terminated most often in the medial portions of the microgyrus or avoided it entirely. There were almost no thalamocortical or corticothalamic projections between the ventrobasal complex and the microgyrus itself, although a dense plexus of thalamocortical fibers was often noted at the border between the malformed and normal cortex. These connectional changes may help explain disturbances in architecture, physiology, and behavior associated with these focal malformations.