This article presents general principles and recent advancements in the clinical application of augmented reality-based navigation surgery (AR based NS) for abdominal procedures and includes a description of our clinical trial and subsequent outcomes. Moreover, current problems and future aspects are discussed. The development of AR-based NS in the abdomen is delayed compared with another field because of the problem of intraoperative organ deformations or the existence of established modalities. Although there are a few reports on the clinical use of AR-based NS for digestive surgery, sophisticated technologies in urology have often been reported. However, the rapid widespread use of video- or robot assisted surgeries requires this technology. We have worked to develop a system of AR-based NS for hepatobiliary and pancreatic surgery. Then we developed a short rigid scope that enables surgeons to obtain 3D view. We recently focused on pancreatic surgery, because intraoperative organ shifting is minimal. The position of each organ in overlaid image almost corresponded with that of the actual organ with about 5 mm of mean registration errors. Intraoperative information generated from this system provided us with useful navigation. However, AR-based NS has several problems to overcome such as organ deformity, evaluation of utility, portability or cost.