The aim of this study was to follow 41 intraoperative perforations of the Schneiderian membrane during sinus floor elevation and to identify potential differences from patients without perforations. Two hundred and one sinus floor elevations were performed at the department of oral and maxillofacial surgery of the University Hospital of Schleswig-Holstein in the years 2005 and 2006. Forty-one intraoperative perforations (20.4%) were documented and treated according to the following scheme: defects smaller than 5 mm were covered with a collagen membrane. Larger defects were additionally sutured. Particulated jawbone mixed 50 : 50 with bone substitute (25 cases) and a 50 : 50 mix of particulated iliac crest bone and BioOss (six cases) mainly served as graft material in the perforation group. In 12 cases, implants were installed at the time of sinus grafting, and in 27 cases, a second operation was performed. Four sinus lift procedures had to be discontinued intraoperatively. Over a mean control interval of 162 days, one implant of the 93 inserted had to be replaced in the perforation group. After 1 year, the implant survival rate was 14 out of 14 in the perforation group vs. 81/92 in the control group. With appropriate treatment, intraoperative sinus membrane perforations did not represent an elevated risk for implant loss, infectious complications or displacement of graft material in the investigated population.