The human motor system undergoes reorganization after amputation, but the site of motor reorganization and the mechanisms involved are unknown. We studied the site and mechanisms of motor reorganization in 16 subjects with traumatic lower-limb amputation. Stimulation at different levels in the CNS was used to determine the site of reorganization. The mechanisms involved were evaluated by measuring the thresholds for transcranial magnetic stimulation (TMS) and by testing intracortical inhibition and facilitation. With TMS, the threshold for muscle activation on the amputated side was lower than that of the intact side, but with transcranial electrical stimulation there was no difference in motor threshold between the two sides.TMS at the maximal output of the stimulator activated a higher percentage of the motor neuron pool (%MNP) on the amputated side than on the intact side. The %MNP activated by spinal electrical stimulation was similar on the two sides. Paired TMS study showed significantly less intracortical inhibition on the amputated side. Our findings suggest that motor reorganization after lower-limb amputation occurs predominately at the cortical level. The mechanisms involved are likely to include reduction of GABAergic inhibition.Key words: amputation; motor reorganization; mechanisms of plasticity; human; transcranial magnetic stimulation; motor cortexThe motor system undergoes reorganization after peripheral nerve lesions Sanes et al., 1990), spinal cord injuries (Lev y et al., 1990;Topka et al., 1991), cortical lesions (Jenkins and Merzenich, 1987;Benecke et al., 1991;Cohen et al., 1991b;Weiller et al., 1992;Nudo et al., 1996), amputations (Hall et al., 1990;Cohen et al., 1991a;Fuhr et al., 1992;Kew et al., 1994;Ridding and Rothwell, 1995), and transient deafferentation induced by ischemia (Brasil-Neto et al., 1992, 1993. The changes after spinal cord injury and transient deafferentation are more prominent with the target muscle at rest than during voluntary activation (Topka et al., 1991;Ridding and Rothwell, 1995). Using ischemic deafferentation of the forearm as a model for short-term plasticity in humans, we recently showed that plastic changes in the deafferented motor cortex can be upregulated by transcranial magnetic stimulation (TMS) to the deafferented cortex and downregulated by TMS to the contralateral motor cortex (Z iemann et al., 1998). Although experiments in animals have shown that reorganization can occur at multiple levels, including the cortex (Pons et al., 1988;Recanzone et al., 1992;Merzenich and Jenkins, 1993; Gilbert, 1994, 1995), thalamus (Garraghty and Kass, 1991;Pons et al., 1991;Nicolelis et al., 1993), brainstem (Pons et al., 1991;Florence and Kaas, 1995), and spinal cord (C arp and Wolpaw, 1994;Florence and Kaas, 1995), the site of motor reorganization in humans is not known. Whereas animal studies have shown that GABAergic (Hendry and Jones, 1986;Welker et al., 1989;Jacobs and Donoghue, 1991), glutaminergic (Anw yl, 1991;Garraghty et al., 1993;Conti et al., 1996), and...