Sinus floor augmentation is one of the most used approaches to obtain sufficient bone availability to place dental implants in cases with severe bone atrophy in the posterior maxilla. Several bone substitutes are indicated for sinus augmentation but they may obtain different clinical outcomes. This study aims to compare bovine bone mineral (BBM) with freeze dried bone allograft (FDBA) in two- stage lateral window sinus grafting approach. 20 patients received a lateral window sinus lift with either FDBA or BBM. Post-operative graft height was measured with a cone-beam computerized tomography (CBCT). 6 months later implants were placed. Biopsies were taken for histological analysis and new CBCts were performed to measure graft height at this point. 6 months after procedure, there was a height reduction of 20,27 ± 4,94 % for the FDBA sample and 5,36 ± 2,41% for the BBM group. The histological analysis revealed a ratio of newly formed bone of 43,70 ± 5,29% for the FDBA and 38,11 ± 4,03% for the BBM group. The FDBA also showed a higher amount of residual biomaterial 17,25 ± 10,10% and connective tissue 14,63 ± 4,38% compared to the BBM 15,53 ± 5,42% and 13,11 ± 4,42%. The differences between groups were statistically significant for the height reduction and for the newly formed bone (p ≤ 0.05) but not for the residual biomaterial amount and the non-mineralized connective tissue (p ≥ 0.05). It could be concluded that the percentage of newly formed bone 6 months after performing a lateral window sinus lift using FDBA was significantly higher than when using BBM, although the graft height reduction was also significantly higher for the FDBA group.