Branemark implant system has been used in Periodontal Department of Taipei Medical University Hospital for more than 13 years and a high ten years accumulative success rate of the system has been reported. However, five cases with retrograde peri-implantitis (RPI) occurred during the treatment period. The following three case reports were briefly the occurrence and clinical management of RPI at the apical sites of implants installed adjacent to incomplete endodontic treated teeth. Two additional implant cases treated with simultaneous prophylactic apicoectomy are also introduced.