Increasing evidence points to the importance of intrinsic molecular cues in specifying the regional identity of mammalian neocortex. Few such cues, however, have been found to be restricted to individual functionally defined cortical areas before the arrival of afferent information. In contrast, thalamocortical axons are specifically targeted to individual cortical areas, raising the possibility that they can instruct some aspects of cortical areal identity. Cortical structure and function can be altered by modifying the source or pattern of activity in thalamocortical afferents. In particular, studies of cross-modal plasticity have shown that in many respects, one sensory cortical area can substitute for another after a switch of input modality during development. Afferent inputs might therefore direct the formation of their own processing circuitry, a possibility that has important implications for brain development, plasticity and evolution.