Sinus floor augmentation is one of the most common approaches to obtain sufficient bone availability for placing implants in cases with severe bone atrophy in the posterior maxilla. Several bone substitutes are indicated for sinus augmentation, but they may achieve different clinical outcomes. This study aims to compare bovine bone mineral (BBM) with freeze-dried bone allograft (FDBA) in a two-stage lateral window sinus grafting approach. Twenty patients received a lateral window sinus elevation with either FDBA or BBM. Postoperative graft height was measured with CBCT. Implants were placed 6 months later, at which time biopsy samples were taken for histologic analysis and new CBCT scans were performed to measure graft height. The mean height reduction at 6 months was 20.27% ± 4.94% for FDBA samples and 5.36% ± 2.41% for BBM samples. The histologic analysis revealed a mean ratio of newly formed bone of 43.70% ± 5.29% for the FDBA group and 38.11% ± 4.03% for the BBM group. The FDBA group also showed a higher amount of residual biomaterial (17.25% ± 10.10%) and connective tissue (14.63% ± 4.38%) compared to the BBM group (15.53% ± 5.42% and 13.11% ± 4.42%, respectively). The differences between groups were statistically significant for the height reduction and newly formed bone (P ≤ .05) but not for the amounts of residual biomaterial and nonmineralized connective tissue (P ≥ .05). Six months after performing a lateral window sinus elevation, the percentage of newly formed bone was significantly higher when using FDBA than when using BBM, although the graft height reduction was also significantly higher for the FDBA group.