The choice of augmentation material is a crucial factor in sinus augmentation surgery. Bovine-derived hydroxyapatite (BHA) and beta-tricalcium phosphate (β-TCP) have been used successfully in sinus augmentation procedures. Choosing one of these materials for sinus augmentation is still controversial. The aim of this clinical study was to compare the biological performance of the new BHA graft material and the well-known synthetic β-TCP material in the sinus augmentation procedure. The study consisted of 23 patients (12 male and 11 female) who were either edentulous or partially edentulous in the posterior maxilla and required implant placement. A total of 23 two-step sinus-grafting procedures were performed. BHA was used in 13 patients, and β-TCP was used in 10 patients. After an average of 6.5 months of healing, bone biopsies were taken from the grafted areas. Undecalcified sections were prepared for histomorphometric analysis. The mean new bone formation was 30.13% ± 3.45% in the BHA group and 21.09% ± 2.86% in the β-TCP group (P = .001). The mean percentage of residual graft particle area was 31.88% ± 6.05% and 34.05% ± 3.01% for the BHA group and β-TCP group, respectively (P = .047). The mean percentage of soft-tissue area was 37.99% ± 5.92% in the BHA group and 44.86% ± 4.28% in the β-TCP group (P = .011). Both graft materials demonstrated successful biocompatibility and osteoconductivity in the sinus augmentation procedure. However, BHA appears to be more efficient in osteoconduction when compared with β-TCP.