Abstract Background Mucous retention cyst refers to a cyst made by expansion due to the blockage of the salivary gland near the maxillary sinus, and it is surrounded by epithelial cells. Most of them are small; therefore, they cannot be found well and are frequently with antral polyp. The aim of this study was to evaluate the clinical prognosis of sinus bone graft in patients with mucous retention cyst. Methods This study was performed retrospectively on 23 patients who had sinus bone graft. Group 1 was 8 patients (10 sinuses) who had a mucous retention cyst, and group 2 was 15 patients (17 sinuses) who had no pathologic history about the maxillary sinus. For these patients, sinus bone graft was performed using the lateral approach technique. The total 51 implants were placed 6.22 weeks on the average after sinus bone graft. Sinus membrane perforation during operation, postoperative complications, marginal bone loss after restorative function, implant success rate, and survival rate were analyzed. Results There was no complication in group 1, and there were three complications in group 2. In group 2, two cases of implants failed. The types of postoperative complications consisted of two minor infections and one wound dehiscence. Two implants of total 51 implants were removed, and the survival rate of implants was 96.08 % (group 1 100 %, group 2 93.5 %). The total success rate of implants was 92.2 % (group 1 95 %, group 2 90.3 %). Conclusions The clinical prognosis was not affected by the presence of mucous retention cyst.