Brainstem-mediated antinociceptive inhibitory reflexes of the temporalis muscle were investigated in 82 patients (47 F, 35 M, mean age 28.3 years, SD 9.4) with acute posttraumatic headache (PH) following whiplash injury but without neurological deficits, bone injury of the cervical spine or a combined direct head trauma on average 5 days after the acceleration trauma. Latencies and durations of the early and late exteroceptive suppression (ES1 and ES2) and the interposed EMG burst (IE) of the EMG of the voluntarily contracted right temporalis muscle evoked by ipsilateral stimulation of the second and third branches of the trigeminal nerve were analyzed and compared to a cohort of 82 normal subjects (43 F, 39 M, mean age 27.7 years, SD 7.1). Highly significant reflex alterations were found in patients with PH with a shortening of ES2 duration with delayed onset and premature ending as the primary parameter of this study, a moderate prolongation of ES1 and IE duration and a delayed onset of IE. The latency of ES1 was not significantly changed. These findings indicate that acute PH in whiplash injury is accompanied by abnormal antinociceptive brainstem reflexes. We conclude that the abnormality of the trigeminal inhibitory temporalis reflex is based on a transient dysfunction of the brainstem-mediated reflex circuit mainly of the late polysynaptic pathways. The reflex abnormalities are considered as a neurophysiological correlate of the posttraumatic (cervico)-cephalic pain syndrome. They point to an altered central pain control in acute PH due to whiplash injury.