Purpose: The aim of this case report is to present a case of incomplete bone formation after sinus augmentation. Methods: A patient having alveolar bone resorption of the maxillary posterior edentulous region and advanced pneumatization of the maxillary sinus was treated with sinus elevation using deproteinized bovine bone in the Department of Periodontology, Kyung Hee University School of Dentistry and re-evaluated with computed tomography (CT) follow-up. Results: Even though there were no significant findings or abnormal radiolucency on the panoramic radiograph, incomplete bone formation in the central portion of the augmented sinus was found fortuitously in the CT scan. The CT scan revealed peri-implant radiolucency in the apical portion of the implant placed in the augmented maxillary sinus. Nevertheless, the dental implants placed in the grafted sinus still functioned well at over 15 months follow-up. Conclusions: The result of this case suggests that patients who received maxillary sinus augmentation may experience incomplete bone formation. It is possible that 1) osteoconductive graft material with poor osteogenic potential, 2) overpacking of graft material that restricts the blood supply, and 3) bone microbial contamination may cause the appearance of incomplete bone formation after sinus augmentation. Further studies are needed to elucidate the mechanism of this unexpected result and care must be taken to prevent it.