This paper describes a method for tracking the camera motion of a real endoscope by epipolar geometry analysis and image-based registration. In an endoscope navigation system, which provides navigation information to a medical doctor during an endoscopic examination, tracking the camera motion of the endoscopic camera is one of the fundamental functions. With a flexible endoscope, it is hard to directly sense the position of the camera, since we cannot attach a positional sensor at the tip of the endoscope. The proposed method consists of three parts: (1) calculation of corresponding point-pairs of two time-adjacent frames, (2) coarse estimation of the camera motion by solving the epipolar equation, and (3) fine estimation by executing image-based registration between real and virtual endoscopic views. In the method, virtual endoscopic views are obtained from X-ray CT images of real endoscopic images of the same patient. To evaluate the method, we applied it a real endoscopic video camera and X-ray CT images. The experimental results showed that the method could track the motion of the camera satisfactorily.