To assess changes in the relationship between cortical motor representation areas and their target muscles following spinal cord lesions, we studied motor evoked potentials (MEPs) to transcranial magnetic stimulation in six patients with complete spinal cord injuries at low thoracic levels and eight healthy subjects. Magnetic stimulation at rest activated a larger fraction of the motoneuron pool and evoked MEPs with shorter latencies from a larger number of scalp positions in muscles immediately rostral to the level of a spinal cord injury than in corresponding muscles in controls. The MEPs associated with maximal voluntary activation were not significantly different in the two groups. These results suggest enhanced excitability of motor pathways targeting muscles rostral to the level of a spinal transection, reflecting reorganization of motor pathways either within cortical motor representation areas or at the level of the spinal cord. The data do not allow the determination of the contribution of spinal or cortical mechanisms. However, they support the notion of a limited flexible relationship between primary motor cortex and its target muscles following alterations of normal input-output patterns.