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The aim of this study was to investigate whether 10Hz repetitive transcranial magnetic stimulation (rTMS) applied over the motor cortex, using a stimulus paradigm employed for pain control in chronic pain, affects acute electrically induced pain. We investigated whether rTMS modulates the nociceptive flexion reflex (NFR) in addition to subjective pain perception. Pain threshold, NFR threshold, supra-threshold NFR response and the concomitant pain intensity and pain unpleasantness visual analogue scale (VAS) scores were compared before and after 20 minutes of rTMS. The effects of 20 trains of 5 seconds duration (55 seconds intertrain interval) of 10Hz rTMS at 80% of the resting motor threshold applied over the dominant motor cortex were compared to sham rTMS in 12 healthy volunteers. Supra-threshold NFR stimulation significantly increased pain unpleasantness VAS scores compared to sham rTMS. There was no significant effect of 10Hz rTMS on the subjective pain threshold or on the NFR threshold and the supra-threshold NFR response. The rTMS paradigm used to control chronic pain is not suitable for controlling Aδ fiber-mediated acute experimentally induced pain since the effects on pain perception were only marginal. There was an increase of the VAS unpleasantness scores but no effect on the NFR. The increased activity of cortico-thalamic projections might modulate the perception of Aδ fiber-mediated pain within the lateral pain pathway. The type of fiber that is stimulated and neuropathic changes in chronic pain are thought to be critical for rTMS to have an effect.