Transanal endoscopic microsurgery (TEM), i.e., the local excision of rectal carcinomas by way of a bimanual operating system with magnified binocular vision, is gaining acceptance in lieu of more radical total interventions. A major issue with this approach is the lack of information on submucosal anatomical structures. This paper presents an advanced navigation system, wherein the intraoperative 3D structure is stably estimated from multiple stereoscopic views. It is registered to a preoperatively acquired anatomical volume based on subject-specific priors. The endoscope motion is tracked based on the 3D scene and its field-of-view is visualised jointly with the preoperative information. Based on in vivo data, this paper demonstrates how the proposed navigation system provides intraoperative navigation for TEM1.