Drug-resistant, neurogenic pain can be treated by chronic motor cortex stimulation using surgically-implanted epidural electrodes. High-frequency, subthreshold repetitive transcranial magnetic stimulation (rTMS) of the motor cortex was shown to be able to produce antalgic effects, at least transiently, in patients with chronic pain. Nevertheless, other cortical targets than the primary motor cortex are tempting (parietal or prefrontal areas for instance) for the management of pain and need to be studied. Motor cortex TMS was also found to modulate non-nociceptive sensory perception as well as acutely provoked pain in healthy subjects by means of a single conditioning pulse or repeated trains. On the contrary, spontaneous or provoked pain was shown to modify motor cortex excitability, as assessed by TMS technique. Taking into account all these observations, it appears that motor cortex function and pain process are closely related and that TMS is a potent tool to explore and to understand this relationship. Beyond this physiological purpose, rTMS could be useful to control episodes of neurogenic pain of limited duration or to select patients for the surgical implantation of a cortical stimulator.