The aim of this study was to evaluate the yield of objective electrophysiological testing of the trigeminofacial system in atypical facial pain (AFP). In addition to the clinical neurological examination, two brainstem reflexes covering both the peripheral parts and the central connections of the trigeminal and the facial nerves, the blink and jaw reflexes (BR and JR), were recorded in 17 AFP patients. The control group consisted of 18 healthy volunteers with no history of facial pain or chronic headache. The AFP patients could be divided into three distinct groups on the basis of the clinical and electrophysiological findings. (1) Major trigeminal neuropathy. Four patients had clinical and electrophysiological signs of trigeminal neuropathy (three patients with an afferent pattern of abnormal BR, and one with absent JR on the clinically affected side) despite normal findings in the MRI-scans of the brain. Thus, electrophysiological testing may be more sensitive than MRI in demonstrating pathology in some of the AFP patients. (2) Minor trigeminal neuropathy. Seven patients had signs of increased excitability of the BR in the form of uni- or bilaterally abnormal (diminished or absent) habituation of the R2 component of the BR; two of these patients also showed clinical signs of trigeminal dysfunction, but the MRI-scans were all normal. This deficient habituation of the BR indicates increased excitability of the BR at brainstem level in nearly 50% of our AFP patients. (3) 'Idiopathic', no signs of trigeminal neuropathy. Five patients had normal findings both in the brainstem reflex recordings and in the clinical examinations. Additionally, one patient had abnormal BAEP and EEG recordings. On the group level, the AFP patients had significantly higher thresholds of the tactile R1 component of the BR than the control subjects. Electrophysiological testing may offer a valuable tool for both the clinical evaluation, and the scientific study of AFP.