We investigated the effect of transcranial magnetic stimulation (TMS) on the brain by focusing on long-term potentiation (LTP) in the rat hippocampus. Male Wistar rats were magnetically stimulated by a round coil positioned over the rat's head. The stimulator delivered biphasic cosine current pulses 238 μs in duration. The peak magnetic fields were set to 0.50 T (motor threshold) at the center of the coil. Rats received 10 1 s trains of 25 pulses/s with a 1 s intertrain interval 4 times per day for 7 days. There was no significant difference between the LTP of the 0.50 T stimulated and sham control groups. The LTP of the 1.25 T stimulated group, however, was inhibited compared with the LTP of the sham control group, suggesting that the synaptic plasticity in the hippocampus was impaired by strong TMS. It is necessary to control the intensity of TMS for maximizing treatment efficacy and safety.