Objective : It has been reported that low frequency repetitive transcranial magnetic stimulation (rTMS) over the unaffected motor cortex improves motor function of the paretic hand in stroke patients by decreasing transcallosal function, which involves bilateral movement. However, it remains to be clarified whether low frequency rTMS deteriorates bilateral movement. In this study, we evaluated the cortico-cortical coupling and the function of bilateral movement after rTMS in stroke patients. Methods : 1 Hz rTMS was applied over the unaffected motor cortex of chronic stroke patients (10 patients, 63.5±8.6 years). Then, we evaluated motor function involving bilateral hands movement and coupling of the cortices by performing electroencephalographic coherence analysis before and after rTMS. Results : We found that rTMS improved acceleration in the paretic hand but deteriorated bilateral movement coordination. The improvement of motor function in the paretic hand lasted for a week after rTMS while the coordination of bilateral movement normalized within 30 min after rTMS. There was no change in the motor function of the intact hand after rTMS. Coordination of bilateral movement has a positive correlation with the coherence of the bilateral hemispheres and the coherence of the supplemental motor cortex and ipsilesional motor cortex. Conclusions : rTMS therapy improved motor function of the paretic hand in stroke patients. However, it temporarily deteriorated bilateral movement coordination. The supplemental motor cortex and ipsilesional motor cortex coupling might help reduce this deterioration in bilateral movement coordination by lessening the coupling between the bilateral hemispheres.