A 38-year-old woman is described with symptomatic strictly right-sided migraine associated with a pontine cavernoma affecting the contralateral (left) nucleus raphe magnus. A persistent facilitation of the right-sided trigeminal nociception was detected interictally using the 'nociception specific' blink reflex, which was more pronounced during the acute attack. This case shows for the first time, an impairment of the anti-nociceptive brainstem nuclei and the facilitation of the trigeminal nociception in the same subject, thus providing further evidence for the key role of the brainstem raphe nuclei in the pathophysiology of migraine.