The objective of this study was to compare the exteroceptive suppression patterns of masseter and temporalis muscles in patients with primary and secondary headache disorders originating from peripheral joint dysfunction. We accomplished the temporalis and masseter exteroceptive suppression in 28 patients with migraine, 25 patients with chronic tension-type headache (CTH), 22 patients with temporomandibular joint (TMJ) dysfunction and 18 healthy controls. The onset latencies and duration of the first suppression period (S1) was not significantly different between the patients and controls. The duration of the second suppression period (S2) was shorter in patients with CTH, migraine (analysed during attack) and TMJ dysfunction than those obtained from controls. A distinctive finding was significantly prolonged onset latency in patients with TMJ over those obtained from patients with CTH and migraine. We concluded that the onset latency of the S2 period is a useful parameter in the differential diagnosis of primary and peripheral headache disorders.