Repetitive training of isolated movements induces reorganization of motor cortical representations. To elucidate the mechanisms of practice-dependent cortical plasticity within the lesioned central motor system at the time of the application of a therapeutic intervention, we examined the effect of repetitive movements on intracortical facilitation (ICF) and inhibition of agonist (extensor carpi radialis [ECR]) and antagonist (flexor carpi ulnaris) muscles of the hand shortly after the movements, by the paired-pulse technique in patients with cortical (n = 9) and subcortical strokes (n = 11). Short intracortical inhibition and ICF were studied by using interstimulus intervals of 2 and 8 milliseconds, respectively, and their interaction with active or passive movement. The active movement produced significantly larger motor-evoked potentials in the ECR muscle in both patient groups. Short intracortical inhibition was particularly decreased after cortical stroke, whereas it was still significant after subcortical stroke. ICF increased significantly after movements compared with rest in the ECR for subcortical stroke patients only. We conclude that repetitive active movements increase the excitability of the motor cortex representing the agonist muscle and interact with intracortical facilitatory circuits in the subcortical stroke group but not in the cortical stroke group. This interaction of circuitry has been reported previously in control subjects and seems to still operate after subcortical stroke during active movement. Alternative networks may be recruited for active movement after cortical stroke. This finding proposes lesion-specific mechanisms of reorganization during the same rehabilitative intervention. Distinct rehabilitative strategies may be required to optimize the activation of the physiologic motor network for different lesions.