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The aim of this study was to investigate 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 and short-term rTMS on brain activity. We investigated the effects of rTMS on P300 latencies by stimulating the supramarginal gyrus (SMG), which is considered to be the area of origin of the P300. As the frequency-dependence of low-frequency rTMS has not been previously investigated in detail, we evaluated the effects of rTMS at frequencies of 1, 0.75 or 0.5 Hz on P300 latencies. The odd-ball task was used to elicit P300s before and shortly after the scalp was stimulated by rTMS. Electroencephalography recordings were measured at the Fz, Cz and Pz electrodes, which were based on the international 10-20 electrode system. We found that 1, 0.75 and 0.5 Hz rTMS affected P300 latencies. 1 Hz rTMS of the left SMG shortened P300 latencies by approximately 25 ms at the Cz compared with the P300 latencies before rTMS. 0.5 Hz rTMS of the left SMG lengthened P300 latencies by approximately 20 ms at the Cz compared with the P300 latencies before rTMS. In contrast, 0.75 Hz rTMS of the left SMG did not affect P300 latencies. These results demonstrate that P300 latencies vary according to the frequency of rTMS.