We investigated the post-train effects of repetitive transcranial magnetic stimulation (rTMS) on motor evoked potential (MEP) size and cortical silent period (SP) duration. rTMS was delivered over the primary motor cortex in trains of 5, 10, 20, 40 and 60 stimuli in normal subjects at rest and in trains of 5, 10 and 20 stimuli during voluntary muscle contraction. The intensity of stimulation was 120% of resting motor threshold. Test MEPs were delivered at different interstimulus intervals after rTMS ended. At rest, 5 Hz trains produced an increase in the MEP size that persisted after the end of the trains. Trains of 5 stimuli produced after-effects that persisted for 0.5 s, whereas trains of 40 and 60 stimuli produced a facilitation that lasted for several seconds. 5 Hz-rTMS delivered during muscle contraction increased the SP duration during stimulation but the increase persisted for only 1 s after the train ended. The present experiments show that the after-effects of rTMS on MEP amplitude and SP duration have different time-courses. rTMS probably elicits its after-effects on excitatory and inhibitory cortical elements through different physiological mechanisms.