The evoked spinal cord potential (ESCP) and the evoked compound muscle action potential (ECMAP) after paired transcranial magnetic stimulation were recorded simultaneously in eight subjects undergoing spine surgery. The ESCP was composed of a short-latency initial wave (D-wave) followed by later waves (I-waves). The mean conduction velocity of each wave was approximately 60 m/s. The interstimulus interval (ISI) affected the amplitude of both ESCP and ECMAP; the amplitude was inhibited at short ISIs (2 ms and 5 ms), was facilitated at ISI of 10 ms, and was inhibited again at longer ISIs (50 ms, 100 ms and 200 ms). The changes in later I-waves were prominent compared to the stable D-wave. These results suggest that transcranial magnetic stimulation alters the excitability of the motor cortex by affecting synaptic transmission in corticomotor (CM) neurons. The inhibition of the motor cortex at longer ISIs may contribute to a silent period following transcranial magnetic stimulation.