BACKGROUND: Low-frequency repetitive transcranial magnetic stimulation (rTMS) has been shown to significantly reduce epileptiform discharges and control clinical seizures in intractable epilepsy patients. The location of epileptic foci and magnetic stimulation sites remain uncertain. The effects of rTMS on electroencephalogram and seizure remain unclear in epileptic patients following dipole source localization. OBJECTIVE: To investigate the effects of low-frequency rTMS on electroencephalogram and seizure in temporal lobe epilepsy patients after dipole source localization. DESIGN, TIME AND SETTING: The randomized, controlled study was performed at the outpatient clinic, Department of Neurology, Hospital Affiliated to North Sichuan Medical College from December 2003 to February 2007. PARTICIPANTS: A total of 30 temporal lobe epilepsy patients, comprising 19 males and 11 females, aged 17-49 years, presented with epilcptiform discharges and were enrolled for this study. Disease course ranged between 1-6 years, with 1-5 seizures per month. Imaging examinations revealed 11 patients with structural changes in the brain. The patients were randomly and equally assigned into drug treatment and transcranial magnetic stimulation (TMS) groups. METHODS: Patients in the drug treatment group were orally treated with carbamazepine. Patients in the TMS group received oral carbamazepine treatment of and TMS. A Maglite-r25 magnetic stimulator (Dantec Dynamics, Denmark) was used to stimulate epileptic foci in the temporal lobe following electroencephalogram dipole localization (1 Hz, 90% threshold intensity, at a stimulation frequency of 500 times, once a day, for 7 days). MAIN OUTCOME MEASURES: At 30 days after TMS, seizure frequency and rate of epileptiform discharges were observed in patients from both groups. Therapeutic safety was investigated during treatment. RESULTS: Within 30 days of treatment, there were no significant differences in seizure frequency between the TMS group (1.5 ± 0.3) seizures and the drug treatment group [(1.9 ± 0.4) seizures] (P > 0.05). The rate of epileptiform discharges [27% (4/15)] was significantly less in the TMS group than in the drug treatment group [73% (11/15)] (P < 0.05). During TMS, five patients suffered from transient mild headache, but were completely relieved within 2 hour. CONCLUSION: Low-frequency rTMS exhibited inhibitory effects on epileptiform discharges over a short period of time, and decreased seizure frequency to some degree. Results from the present study suggested that low-frequency rTMS is safe.