We employed magnetic stimulation to study the masseter silent period (SP) in 16 healthy volunteers. Cutaneous perception threshold (CPT or 1 T) was determined. SP threshold was 30% M (maximal output) in each subject, equivalent to 1.5-3 T, and as intensity increased, SP durations prolonged. The correlation was higher with units of % M (r = 0.89) than CPT (r = 0.39). The recommended intensity was 60% M because of least variation of SP durations. Conclusively, magnetic stimulation is a new and painless method to study masseter SP. CPT is less effective in studying masseter SP with magnetic stimulation as the input effectiveness correlates best with % M rather than CPT.