The effects before and after repetitive transcranial magnetic stimulation (rTMS) on EEG activity were investigated. Nineteen healthy subjects received two trains (10 Hz, 100% of motor threshold, 3 s/train) of rTMS to the left frontal area. Directed coherence and ordinary coherence were calculated from EEG epochs recorded before and after (1 approximately 3 and 3 approximately 5 min) rTMS. The results were compared and demonstrated on maps. Directed coherence between cortical areas increased after rTMS (F=5.62, P<0.005), with the intra-hemispheric change being more pronounced than the inter-hemispheric change. Connections from the stimulated site to other sites were selectively reinforced. In contrast, ordinary coherence did not change after the stimulation. rTMS did not influence the dominant frequency at which maximal coherence was calculated. Differences in the directed coherence with opposite directions after rTMS were significantly correlated with the differences before rTMS (r=0.88, 0.89, P<0.001). (1) rTMS can enhance the connections between cortical areas, especially connections between the stimulated cortex and other sites in the brain. (2) Comparing with connections from the parietal area to frontal area, connections from the frontal area to parietal area are obviously improved by rTMS in both hemispheres. (3) The effects of rTMS can last for several minutes. Therefore, the necessity of EEG monitoring in rTMS studies is suggested.