Abstract-Despite rapid developments in the research areas medical imaging, medical image processing and robotics, the use of computer assistance in surgical routine is still limited to diagnostics, surgical planning, and interventions on mostly rigid structures. In order to establish a computer aided workflow from diagnosis to surgical treatment and follow-up, several proposals for computer assisted soft tissue interventions have been made in recent years. By means of different pre-and intraoperative information sources, like surgical plannings, intraoperative imaging, and tracking devices, surgical navigation systems aim at supporting surgeons in localizing anatomical targets, observing critical structures, and sparing healthy tissue. Current research in particular addresses the problem of organ shift and tissue deformation, and obstacles in communication between navigation system and surgeon.In this article, we review computer assisted navigation systems for soft tissue surgery. We concentrate on approaches which can be applied in endoscopic thoracic and abdominal surgery, as endoscopic surgery has special needs for image guidance due to limitations in perception. Furthermore, this article provides the reader with new trends and technologies in the area of computer assisted surgery. Finally, a balancing of key challenges and possible benefits of endoscopic navigation refines the perspectives of this increasingly important discipline of computer aided medical procedures.