Intraoperative imaging during skull-base surgery allows the operator to control surgical dissection and to tailor the approach, reducing morbidity due to inadequate resection or reintervention. The O-arm® (Medtronic, Fridley, MN, USA) navigation system is an intraoperative cone-beam CT device that was first designed for spinal surgery but now has applications in lateral skull-base surgery. In this technical note, we present a patient with petrous apex cholesterol granuloma located medial to the intrapetrous internal carotid artery and in the infralabyrinthine compartment. We report the possibility of natural drainage, using intraoperative imaging to guide resection, through a rapid, safe and minimally invasive approach.