Dorsolateral prefrontal cortex (DLPFCx) has been implicated in pain perception and in a pain modulation pathway. However, the precise participation of this region is not completely understood. The aim of this study was to evaluate whether 1 Hz rTMS of DLPFCx modifies threshold and tolerance in experimental pain. The effect of 1 Hz rTMS during 15 min at 100% motor threshold was tested in one hundred and eighty right-handed healthy volunteers, using a parallel-group stimulation design. The stimulation sites were right or left DLPFCx, right or left motor cortex, vertex or sham. rTMS was applied in two experimental contexts: (1) To evaluate its transitory effect (interference or facilitation) during cold pressor threshold (CPTh) and tolerance (CPTt) and (2) to evaluate its long-term effect by stimulating before CPTh, CPTt, pain heat thermal threshold, pain pressure threshold and tolerance. During rTMS of right DLPFCx, an increase in left hand CPTt (mean +/- SD; 17.63 s +/- 5.58 to 30.94 s +/- 14.84, P < 0.001) and in right hand CPTt (18.65 s +/- 6.47 to 26.74 s +/- 11.85, P < 0.001) were shown. No other stimulation site modified any of the pain measures during or after rTMS. These results show that 1 Hz rTMS of right DLPFCx has a selective effect by increasing pain tolerance and also sustains a right hemisphere preference in pain processing.