Image-guided navigational systems have been a useful adjunct for minimally invasive surgery of the skull base. A novel miniature position sensor has been developed that uses a low magnetic field for real-time tracking of surgical instruments. The 1.7-mm-diameter sensor attached to the position and orientation system (Magellan®, Biosense, Inc., Johnson and Johnson Co., Baldwin Park, CA) was deployed through various surgical instruments or used in a hand-held fashion with a malleable shaft probe. We report on our experience using this electromagnetic system in a series of lesions of the sella and clivus. After patient/image registration, the system was consistently accurate to within 2 mm. We have found this system to be particularly advantageous in endoscopic surgery of cystic lesions of the skull base, where access is limited and anatomy may be distorted. In three patients, this device obviated the need for an extensive external surgical approach. Case histories are presented, which illustrate the specific advantages this miniature system provides during skull base surgery.