It is well known that a silent period (SP) can be observed in voluntary tonic EMG activity starting directly after the initial early response when magnetic stimuli are delivered through the skull over the contralateral primary motor cortex. It is, however, unknown as to how an individual motoneurone (MN) contributes to the SP observed in the surface EMG. The present investigation was conducted to investigate inhibitory phenomena at the level of individual motor units. It demonstrates that the duration of the SP in single motor units is inhomogeneously distributed within the pool of active MNs. At various stimulation strengths, SP durations in single motor units can be similar or longer when compared to that observable in surface EMG records. In some motor units, which show low thresholds for early excitation and appearance of the SP, durations of SP can exceed 1000 msec. The length of suppression of spontaneous MN firing is maximal at stimulus intensities a little higher than those required for an early excitatory response. Although in general thresholds for early excitation and appearance of SPs are similar, at threshold stimulation in a number of trials inhibitory effects on the firing of voluntarily activated motoneurones were present, even in the absence of early excitations. This proves the independent nature of inhibitory as opposed to excitatory effects induced by transcranial magnetic stimulation. An SP in the absence of early excitation underlines its cortical origin. Inhibition and excitation of single MNs were maximal over the same small scalp area. We suggest that cortical inhibitory control plays an important role in the organization of natural movements.