We retrospectively reviewed the clinical experience of 30 patients with brain stem cavernous malformations (BSCM) treated operatively and non-operatively at our hospital between 1983 and 2005 to elucidate the natural history of BSCM and the factors that affect surgical outcome. Inpatient charts, imaging studies, operative records, and follow-up results were evaluated. The average follow up was 48.5 months. Twenty-two patients (73.3%) received surgical extirpation and of these 86.4% improved or stabilized and 13.6% deteriorated with permanent or severe morbidity. There was no mortality. Size, preoperative status, and surgical timing were factors related to surgical outcome. In the non-operative group, 50% of the patients were the same or better, 25% deteriorated, and 25% died. With appropriate patient selection, resection of BSCM can be achieved with acceptable morbidity compared with the ominous natural history of these lesions.