Systems and methods of tracking the position of an endoscope within a patient's body during an endoscopic procedure is disclosed. The devices and methods include determining a position of the endoscope within the patient in the endoscope's coordinate system, capturing in an image fiducial markers attached to the endoscope by an external optical tracker, transforming the captured fiducial markers from the endoscope's coordinate system to the optical tracker's coordinate system, projecting a virtual image of the endoscope on a model of the patient's organ, and projecting or displaying the combined image.
