In recent years the application of 3D video endoscopic systems in clinical routine, especially in the field of endoscopic surgery, has increased steadily. The number of 3D video endoscopic systems used in the operating theatre today is obviously lower than the number of established traditional 2D video endoscopic systems. The hesitant application of the new technology can be mainly explained by the lack of evaluation of its influence on the surgical procedure and on patient benefit as well as by the need for specific economic analysis. The starting point for our investigations was to analyze the influence of 3D video endoscopy on endoscopically guided manipulations in general. In order to achieve quantitative statements we performed laboratory experiments using human factors analyzing methods. In the next step we performed clinical field studies of the application of 3D video endoscopic systems for a side-by-side comparison of 2D and 3D systems. These studies showed that the use of 3D video endoscopy has an improving influence on endoscopically guided surgical manipulations as well as on the intraoperative procedures. We also found that spatial visual perception of stereoscopic images of 3D video systems may cause problems for some users. For the validation of stereoscopic visualization systems we additionally studied the influence of isolated technical, optical, and physiological parameters on visual perception as well as on transposition into visually guided manipulations. Detailed results of these investigations concerning the influence of 3D video endoscopy on binocular perception are presented.