We have examined input-output patterns in the corticospinal system after incomplete spinal cord injury. The amplitude of the motor evoked potential (MEP) to transcranial magnetic stimulation (TMS) was used to study the patterns of recruitment, with increasing stimulus intensity, and facilitation, with increasing voluntary contraction, in thenar muscles of 12 patients with incomplete spinal cord injuries and 13 control subjects. The patients had all suffered spinal cord injury at a segmental level rostral to C8 and T1, the segments supplying innervation of thenar muscles. The patients showed a less pronounced increase in MEP amplitude with increasing strength of TMS compared with the controls. Specifically, at a stimulus strength of 120% threshold and above, the patients showed significantly smaller MEPs relative to the maximum ulnar nerve M-wave response than the controls. The patients also showed a less steep pattern of facilitation with voluntary drive. The MEP continued to increase up to 50% maximum voluntary contraction (MVC) whereas the controls reached a plateau around 10% MVC. The results indicate that the patients show modified corticospinal recruitment and facilitation of the motoneurone pool. We speculate that the function of the adapted corticospinal system after spinal cord injury might be to regulate and modulate drive to motoneurones originating from segmental and other descending inputs. We discuss how such a modified corticospinal system might be of functional benefit to the patients.