We report a 32-year-old woman who presented with headache, mild hemiparesis and clumsiness of the right hand. CT and MRI revealed a multicystic formation of the brainstem involving the thalamus and midbrain. We inspected the formation endoscopically and fenestrated some of the cysts. In one of the cysts we found an anomalous vascular nidus. Postoperative MRI revealed reduction of the fenestrated cysts. The patient is doing well 13 months after endoscopy and has no neurological deficit.