Aims: To report the incidence of infectious and noninfectious endophthalmitis after intravitreal injection of anti-vascular endothelial growth factor (VEGF) from a multicenter clinical trial in Japan. Methods: A retrospective multicenter review of the data of patients who received intravitreal anti-VEGF injections between January 2007 and March 2011 was undertaken. Cases with the clinical diagnosis of endophthalmitis resulting from intravitreal injection were identified and reviewed. Results: A total of 5,236 intravitreal anti-VEGF injections (1,209 intravitreal injections of bevacizumab, 3,827 injections of ranibizumab, and 200 injections of pegaptanib sodium) had been administered. Five patients (0.095%), all of whom had received bevacizumab, were diagnosed as having endophthalmitis after the intravitreal injection. All patients visited the institutes for re-examination within 1–2 days after the injection. Among the 5 patients, 2 (0.038%) were culture positive for Streptococcus oralis and Enterococcus faecalis, respectively. The remaining 3 eyes (0.057%) developed presumed noninfectious endophthalmitis. Conclusion: Although endophthalmitis is a rare complication associated with intravitreal injection, in this series intravitreal anti-VEGF injection caused infectious or noninfectious endophthalmitis at a relatively high frequency. Further investigations are needed to consider an appropriate injection protocol for minimizing the incidence rates of endophthalmitis, and to assess the optimal treatment protocol for intravitreal injection-related endophthalmitis although it was difficult to differentiate these two entities.