Repetitive transcranial magnetic stimulation (rTMS) was shown to have therapeutic potential for some neurological and psychiatric disorders. Previous studies reported that low-frequency rTMS (</=1 Hz) affected synaptic plasticity in rats, however, there were few investigations to examine the possible effects of rTMS on structural synaptic plasticity changes in rats, which included the effects on synaptic morphology in the hippocampus, synaptic protein markers and Ca(2+)/calmodulin-dependent protein II (CaMKII). Sprague-Dawley rats were subject to 500 pulses of 0.5 Hz rTMS for 15 days, or sham stimulation. After last stimulation, transmission electron microscope (TEM) and real-time PCR were used to determine the effects of rTMS on synaptic plasticity. Results showed that rTMS could cause the change of structural synaptic plasticity, increase the expression of synaptic protein markers: synaptophysin (SYN) and increase the expression of CaMKII, relative to normal rats. suggesting a modulatory effect of chronic rTMS on synaptic plasticity that may be attributed to the increased expression of CaMKII in rats.