The loss of sensory inputs after nerve damage or the loss of a limb in the mature somatosensory system is followed by a gradual reactivation of parts of the system, such as primary somatosensory cortex, that had been devoted to the missing sensory input. This recovery appears to be the result of a number of neural mechanisms, including the growth of new connections at several levels of the somatosensory system. Some of this new growth and recovery occurs at the levels of the brainstem and thalamus, and the changes are relayed to cortex. This kind of reorganization can lead to misperceptions (touch on one skin surface is often perceived as on another) and phantom pain. This detrimental reorganization can be altered in several ways. Most importantly, the transplantation of a hand to replace an amputated hand can lead to reinnervation of the hand and the recovery of a more normal somatosensory and motor system. Other types of cortical reorganization after peripheral injury may lead to improvements in sensory and motor abilities based on the greater representation of remaining inputs.

Another type of injury, a lesion of motor cortex, results in an inactivated area of cortex. The size of the non-functional area of motor cortex increases during the period immediately following the lesion. This can be prevented or even reversed by treatments that involve training and increased use of the impaired limb. With training, the reduced representation of the impaired limb increases in extent in damaged motor cortex, partially compensating for the damage that removed part of the limb representation.

Finally, motor cortex reorganizes after the loss of a limb to increase the representation of preserved muscles in the limb stump and adjoining body parts. This reorganization may have some useful consequences for improved use of the preserved muscles, and it is based in part on changes in peripheral nerve connections, as well as adjustments in central nervous system connection strengths.