OBJECTIVE To evaluate the differences in the recovery cycle of the masseter inhibitory reflex (MIR) obtained with electrical and magnetic stimulation. METHODS In 31 healthy subjects we studied the MIR evoked by electrical or magnetic stimulation of the mental territory and the recovery cycle of this reflex with the paired stimuli technique at different interstimulus intervals (ISI), between 100 and 600 ms. RESULTS Latency and area of the early and late silent periods (SPs) of the MIR were similar after electrical and magnetic stimulation. The recovery cycle of the test late SP was similar with the two kinds of stimulation, except for short ISIs. The main difference between the two kinds of stimulation was in the painful quality of the stimulus: the magnetic stimuli were always below pain threshold. CONCLUSIONS As with electrical stimulation, it is possible to obtain a MIR with magnetic peripheral stimulation. The magnetic paired stimuli are equally effective in the evaluation of the recovery cycle of the MIR. The results demonstrate that magnetic stimulation is a useful tool in the evaluation of excitability of the trigeminal motoneuronal system, with little discomfort for the patient. They also confirm the unlikelihood of nociceptive afferences involvement.