Purpose: To compare three different lateral sinus elevation procedures concerning new bone formation by using micro-computed tomography (micro-CT) of retrieved implants. Materials and Methods: Twenty-four consecutive partially dentate patients with a mean age of 64 years were included in the study and provided with 30 sinus elevation procedures. Three procedures for lateral sinus elevation were used: lateral sinus elevation with replacement of bone window and without bone graft (BW), lateral sinus elevation and covering osteotomy site with a collagen membrane and without bone graft (CM), and lateral sinus elevation with autogenous bone graft (ABG). Experimental implants were retrieved after 7 months of healing and analyzed by micro-CT. Results: One implant was found not to be integrated at the time of implant retrieval. This implant belonged to group CM and was excluded when calculating bone-to-implant contact (BIC) and intrasinus bone levels. The integrity of the lateral sinus bony wall was determined at the time of implant removal. In group ABG, all lateral sinus walls were ossified. In group BW, one lateral sinus wall was not completely ossified and in group CM, two lateral sinus walls. There were no statistical differences in %BIC between the groups: 93.5% (BW), 92.0% (CM) and 93.5% (ABG). Additionally, no statistical differences were found in apical intrasinus bone levels between the groups. When surfaces were compared within the same implant, a statistical difference was found between the apicobuccal distance and the apicolingual distance. The mean apicobuccal distances/apicolingual distances were 0.6 mm/1.2 mm for the BW group, 0.5 mm/0.8 mm for the CM group, and 0.6 mm/0.8 mm for the ABG group (P = .003). Conclusions: All three procedures were statistically equal when new bone formation was compared. Most of the examined implants' apices were not covered with bone at the time of retrieval.