It is known that the execution of the motor response in a simple reaction time (RT) task can be delayed by transcranial magnetic stimulation (TMS). This paper is aimed at determining the site of action where the delay in RT occurs. A delay in RT was obtained only at those TMS sites over the motor cortex contralateral to the responding hand, which produced also a muscle twitch in the responding hand. The delay in RT covaried with the TMS intensity and increased the closer the time of TMS approached the expected time of reaction onset. Visual and auditory go-signals yielded similar delays in RT, but only when TMS was applied about 40 ms later for the visual go-signal, corresponding to the modality specific difference in RT control values. TMS of the supplementary motor area (SMA) immediately prior to the expected time of reaction onset produced no delay in RT. Spinal excitability as tested by F waves showed a pre-movement facilitation in the control trials which continued seemingly undisturbed during the period of RT delay after TMS. It can be concluded that the delay in RT is not due to SMA stimulation or spinal inhibition but depends on effective stimulation of neural elements in the motor cortex which are active very late in the process of movement release from the final motor output stage.