Colloid cysts appear most commonly in the third ventricle; the occurrence of a colloid cyst in the brainstem is very unusual. The authors report on a patient with an intrapontomesencephalic colloid cyst. This 15-year-old girl complained of a headache associated with diplopia. Her neurological examination revealed right-sided sixth nerve paresis and a mild left hemiparesis. Radiological investigations revealed an intraparenchymal pontomesencephalic cystic mass. Surgical removal of the lesion was achieved via the pterional transsylvian approach and the patient experienced an excellent recovery. Histopathological examination revealed that the lesion was a typical colloid cyst. To the best of the authors' knowledge, this is the first case in which an intraparenchymal upper brainstem colloid cyst was surgically excised totally. In addition to describing this case, the authors also review other brainstem neuroepithelial cysts described in the literature and briefly discuss the concept of their origin.