We studied cortical activation patterns by functional MRI in a patient who received bilateral hand transplantation after amputation 6 years ago. In the early post-operative period, the patient who had had the hand transplantation revealed strong activation of a higher motor area, only weak activation of the primary sensorimotor motor cortex and no activation of the primary somatosensory cortex. At one-year follow-up, a small increase in primary sensorimotor motor cortex activation was observed. Activation of the primary somatosensory cortex was only seen at the 2-year follow-up. Transplantation after long-standing amputation results in cortical reorganisation occurring over a two-year period.