To evaluate reorganization in motor pathways following amputation, we studied motor evoked potentials (MEPs) to transcranial magnetic stimulation in 7 patients with unilateral upper limb amputations, a patient with congenital absence of a hand, and 10 normal subjects. Electromyographic recordings were made from biceps and deltoid muscles immediately proximal to the stump and the same contralateral muscles. Magnetic stimulation was delivered by a Cadwell MES-10 magnetic stimulator through a 'figure eight' magnetic coil over scalp positions separated by 1-2.5 cm. Maximal M responses were elicited by peripheral nerve stimulation at Erb's point. The amplitude of MEPs was expressed both as absolute values and as a percentage of maximal responses to peripheral nerve stimulation. Threshold for activation of muscles ipsilateral and contralateral to the stump and the region of excitable scalp positions were also determined in 7 patients. Magnetic scalp stimulation induced a sensation of movement in the missing hand or fingers in the patients with acquired amputation, but failed to do so in the patient with congenital absence of a limb. It evoked larger MEPs, recruited a larger percentage of the motoneuron pool, and elicited MEPs at lower intensities of stimulation in muscles ipsilateral to the stump than in contralateral muscles. Muscles ipsilateral to the stump could be activated from a larger area than those contralateral to the stump. These results are compatible with cortical or spinal reorganization in adult human motor pathways targeting muscles proximal to the stump after amputations.