The cortical cytoarchitecture, cortical thickness, corticostriatal connections, cortical dendritic arborization, and striatal patch-matrix compartmentalization were compared in rats with neonatal (1 day of age) or adult hemidecortication. Neonatal hemidecortication produced few changes in cytoarchitecture of the remaining hemisphere and did not preclude the development of a patch-matrix compartmentalization in either striatum. There was a significant modification of contralateral cortical-striatal connections, however, as there were extensive crossed connections from layer II/III of the prefrontal cortex in the neonatal hemidecorticates, which contrasts with connections from layer V in the normal brain. Adult hemidecorticates had no crossed corticostriatal connections. Neonatal hemidecortication also led to an increase in cortical thickness relative to adult operates or controls and the neonatal hemidecorticates, and led to an increase in dendritic arborization in layer II/III pyramidal cells of the somatosensory and motor cortex but not in the visual or temporal cortex. The results suggest that the behavioral sparing of sensorimotor and some prefrontal functions after neonatal hemidecortication could be supported, in part, by the anatomical changes in the prefrontal and sensorimotor connectivity and dendritic arborization.