The advent of electronic medical records brought image filing systems to many hospitals, as well as electronic endoscopic medical records. However, data integration among multiple different vendors has not yet been accomplished. We start the Japan Endoscopic Database (JED) Project endorsed by Japan Gastroenterological Endoscopy Society (JGES) from January 2015. The purposes of this project are as follows: (i) developing the world's largest endoscopic database generated from daily use of the reporting system; (ii) capturing the actual performance of endoscopic practice in Japan; and (iii) standardizing the terminology and fundamental items for registry of clinical studies. Moreover, the JED project has the potential to automatically collect data about adverse events, competency and evaluation of residents, and actual numbers of procedures on a nationwide scale, certification for the specialty board system, and so on. We believe that this design paper will be helpful not only for future nationwide research but also for international research (UMIN000016093).