The aim of the present study was to assess reorganization in the motor cortex of patients with lower limb amputation. We studied seven patients with traumatic lower limb amputation, and six healthy controls, using transcranial magnetic stimulation mapping, with recordings from the quadriceps femoris muscle on both sides. Motor threshold, sum of amplitudes, area and the amplitude-weighted centre of gravity (COG) of the motor output map were assessed. We found a significant lateral displacement of the COG on the hemisphere contralateral to the healthy leg, whereas other parameters did not differ significantly between sides. This finding might be indicative of cortical reorganization in the hemisphere ipsilateral to the amputation. It is discussed with respect to an altered peripheral input to this hemisphere, and to transcallosal interactions from the deafferented hemisphere.