OBJECTIVE: The aim of this study is to identify the ipsilateral motor evoked potentials (iMEPs) from unaffected cerebral hemisphere after stroke via transcranial magnetic stimulation, especially in acute stage (within 1 week from attack), and to evaluate the characteristics of iMEPs compared with the crossed contralateral motor evoked potentials (cMEPs). METHOD: Thirty patients were recruited, who had suffered their first ischemic stroke and consequent motor deficits and mean duration from attack to examination was 6.0 3.3 days. They were tested with round coil stimulator in order to record motor evoked potentials from both contralateral and ipsilateral abductor pollicis brevis (APB) muscles. For the purpose of hand motor cortex mapping, we designed specialized cap, which was marked using international 10-20 systems by 1 cm interval. In addition, we observed the changes in onset latency and amplitude of MEPs during the isometric contraction of thenar muscle guided by visual and auditory feedback. RESULTS: iMEPs were generally absent in normal subjects, but they were obtained in 17 (56.7%) of 30 patients by stimulating the unaffected hemisphere. Different from contralateral MEPs, ipsilateral MEPs were obtained with higher stimulation intensity, significantly delayed latencies and lower amplitudes. And we noticed shorter latencies and larger amplitudes of MEPs by the isometric contraction of thenar muscle. CONCLUSION: Our results will reflect the compensatory role by the unaffected cerebral hemisphere with respect to motor recovery, if contralateral route is damaged. We provided neurophysiologic evidences of cerebral neuroplasticity, proven by the ipsilateral unaffected hemispheric activation in early phase stroke patients.