Maxillary sinus grafting is generally a safe procedure. However, intraoperative complications, as well as early and late postoperative complications, may occur. Included in the latter group are graft infections that can be triggered by peri-implantitis. The aim of the present study was to report three cases of late maxillary sinus graft infections and to histologically evaluate the effects of peri-implantitis in the grafted area. In peri-implantitis cases in grafted sinuses, the sole removal of the implant along with accompanying debridement of the infected area may not be sufficient to resolve the infection, and a more-aggressive treatment may be necessary.