In 22 healthy subjects, painless repetitive transcranial magnetic stimulation (rTMS) was used to investigate the role of the cortex in the regulation of pupil size and the influence of TMS on the central autonomic nervous system. RTMS was performed over three brain regions of each hemisphere (frontal, central, parieto-occipital), over cervical nerve roots and in front of the ear (sham stimulation) while the size of the pupil was measured by infrared oculography. rTMS always elicited a dilatation of both pupils, with its maximum after approximately 1.5 s and without significant R–L difference in latency or amplitude of pupillary response. No differential effects were observed for stimulation over different cortex regions of one hemisphere, but stimulation over the right central region evoked a larger dilatation of the pupil than stimulation over the left. Pupillary dilatation was larger for cervical nerve root stimulation (+13.2±8.3% (S.D.) of baseline) than for suprathreshold cortex stimulation (+8.4±4.5%, five 10-Hz stimuli). Pupillary dilatation in response to magnetic cortex stimulation appears to reflect a mainly unspecific activation of the sympathetic system rather than an activation of a cortical pupillomotor centre. Sympathetic activation following rTMS of the cortex does not limit its experimental and therapeutic application.