Accurate patient registration and referencing is a key element in navigated surgery. Unfortunately all existing methods are either invasive or very time consuming. We propose a fully non-invasive optical approach using a tracked monocular endoscope to reconstruct the surgical scene in 3D using photogrammetric methods. The 3D reconstruction can then be used for matching the pre-operative data to the intra-operative scene. In order to cope with the near real-time requirements for referencing, we use a novel, efficient 3D point management method during 3D model reconstruction. The presented prototype system provides a reconstruction accuracy of 0.1 mm and a tracking accuracy of 0.5 mm on phantom data. The ability to cope with real data is demonstrated by cadaver experiments.