Earlier investigations have shown that stimulation of peripheral afferent nerves induces prolonged changes in the excitability of the human motor cortex. The present study compared the effect of experimental pain and non-painful conditioning stimulation on motor evoked potentials (MEPs) elicited by transcranial magnetic stimulation (TMS) in the relaxed first dorsal interosseous (FDI) and flexor carpi ulnaris (FCU) muscles. The MEPs were measured in 10 healthy subjects, and stimulus-response curves were generated before and after each of four stimulation paradigms conducted in random order on separate occasions: (a) control; (b) "dual stimulation" consisting of electrical stimulation of the FDI motor point paired with TMS; (c) painful infusion of hypertonic saline in the FDI muscle; and (d) pain combined with dual stimulation. There were no significant changes in FDI MEPs following the control paradigm, and dual stimulation induced an increase in the FDI MEPs only inconsistently. In contrast, the painful stimulation and the combined pain and dual stimulation paradigms were followed by significant suppression of the FDI MEPs at higher stimulus intensities. No changes were observed in the FCU MEPs following the four paradigms. In two additional subjects, the responses evoked in FDI by direct stimulation of the descending corticospinal tracts were significantly depressed following painful stimulation of the FDI, although the ulnar-evoked M-waves remained constant. It is concluded that muscle pain is followed by a period with profound depression of MEPs amplitudes in the resting muscle, but that these changes are at least in part due to a lasting depression of the excitability of the motoneurones in the spinal cord. Hence, painful stimulation differs from non-painful, repetitive stimulation, which facilitates the corticomotor pathway.