Transcranial magnetic stimulation (TMS) of the motor cortex during tonic muscle contraction produces a motor evoked potential followed by a silent period in the electromyogram. We sought to characterise the TMS induced silent period and to compare it to the silent period induced by supramaximal peripheral nerve stimulation. TMS was delivered to the motor cortex using a 9 cm diameter circular coil and the surface electromyogram was recorded from the contralateral abductor pollicis brevis muscle in six normal subjects. Increasing TMS stimulus intensity from 10 to 50% above threshold resulted in an increase in the duration of the silent period from a mean of 50 ms to 185 ms. Increasing the level of tonic muscle contraction from 5% of maximum to maximum resulted in a decrease in silent period duration from a mean of 155 ms to 133 ms. In contrast, the duration of the silent period following supramaximal median nerve stimulation showed greater shortening under similar conditions, from a mean of 160 ms at 5% of maximum contraction to 99 ms at 75% of maximum contraction. The TMS induced silent period was present during a TMS induced increase in the reaction time for a ballistic movement, the onset of movement being delayed until the end of the silent period. Peripheral nerve stimulation did not produce a delay in movement onset. The present findings favour a cortical origin for the TMS induced silent period, probably on the basis of intracortical inhibition, rather than peripheral inhibition of spinal motoneurones which is considered to be the basis for the silent period following peripheral nerve stimulation.