To prospectively survey the incidence of endophthalmitis following cataract surgery and investigate the current perioperative practices in Japan. Patients who underwent cataract surgery from January 2012 to December 2013 were included. Information on perioperative practices were recorded prospectively. Clinical characteristics were examined in cases with endophthalmitis. A total of 63,244 patients who underwent cataract surgery in 205 facilities were enrolled. The detailed information about the current perioperative scenario surrounding cataract surgery in Japan was evaluated for the preoperative, intraoperative, and postoperative practices, i.e., patient background, prophylactic antibiotic regimen, modes of disinfection or disinfectant use, preoperative procedure, surgical method, surgical materials, surgical complication, or others. Postoperative endophthalmitis developed in 25 patients within 8weeks postoperatively (incidence 0.04%). However, since outbreaks of toxic anterior segment syndrome (TASS) after implantation of intraocular lenses contaminated with aluminum (HOYA iSert 251 and 255) were reported, 10,261 cases implanted with the lenses had been excluded (as having a risk for non-infectious late-onset TASS). In the remaining 52,983 cases, postoperative endophthalmitis developed in 13 cases within 8weeks postoperatively (incidence 0.025%). This prospective survey identified the current perioperative practices representing cataract surgery and the incidence of endophthalmitis following cataract surgery (0.025%) in Japan. We believe this information can serve as a guide for future improvement in risk-reduction strategies.