Transcranial magnetic stimulation (TMS) is a non-invasive and painless method to stimulate the cortex. Accurate estimation of stimulating points is much important to evaluate cortical functions such as cortical motor output maps. However, most studies using TMS have not achieved to estimate the stimulating points exactly. This study proposed the novel method to provide the accurate estimation of stimulating points of the cortex in TMS taking account of the individual cortical anatomy and property of nerve excitation. We conducted TMS mapping of the motor cortex to confirm the validity of this method. The cortex sites which innervate muscles of the upper limb and hand were successfully delineated in primary motor area