This paper presents a new pq-space based 2D/3D registration method for camera pose estimation in endoscope tracking. The proposed technique involves the extraction of surface normals for each pixel of the video images by using a linear local shape-from-shading algorithm derived from the unique camera/lighting constrains of the endoscopes. We demonstrate how to use the derived pq-space distribution to match to that of the 3D tomographic model, and demonstrate the accuracy of the proposed method by using an electro-magnetic tracker and a specially constructed airway phantom. Comparison to existing intensity-based techniques has also been made, which highlights the major strength of the proposed method in its robustness against illumination and tissue deformation.