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In the present study, we analyzed the effects of repetitive transcranial magnetic stimulation (rTMS) on brain activity. The latency of the P300 component of the event-related potential (ERP) was used to evaluate the effects of low-frequency rTMS following stimulation of the dorsolateral prefrontal cortex (DLPFC), which is an area considered to be related to the generation of the P300. In addition, prolonged stimulation effects on the P300 latency were analyzed after applying rTMS. A figure-eight coil was used to stimulate the left or right DLPFC, and the intensity of magnetic stimulation was 80% of the motor threshold. A total of 100 magnetic pulses were applied for the rTMS. The effects of stimulation at frequencies of 0.5 or 1 Hz were determined. An odd-ball task was performed before and 5, 10, and 15 minutes after rTMS to measure the effects of rTMS on the P300. Electroencephalography (EEG) was measured at the Fz, Cz and Pz electrodes using the international 10-20 electrode system. We found that 0.5 and 1 Hz rTMS produced different effects on P300 latencies. 1 Hz stimulation of the left DLPFC lengthened P300 latencies by approximately 20 ms at the Cz, which lasted up to 15 minutes post-rTMS. In contrast, 0.5 Hz rTMS stimulation of the left DLPFC and 0.5 and 1 Hz rTMS stimulation to right DLPFC had no significant effects on P300 latencies. These results demonstrate that the effects of rTMS on the P300 latency depend on the frequency of stimulant and the area stimulated. Furthermore, we have determined the duration of this effect of low-frequency and short-term rTMS.