Purpose: To compare the tissue composition of augmented sites after using two different synthetic bone substitute materials, nanocrystalline and nanoporous hydroxyapatite (HA), for sinus floor elevation and augmentation. Materials and Methods: Forty-four patients received 88 titanium screw implants (Camlog Promote plus) of 4.3-mm diameter and 11- or 13-mm length, placed simultaneously during sinus floor elevation and augmentation. Nanocrystalline (Ostim) or nanoporous (NanoBone) HA were used exclusively. Bone substitute materials and implant lengths were allocated by randomization. Bone biopsy specimens were obtained from the former area of the lateral access window at implant exposure during healing abutment placement after 6 months. Biopsy specimens were prepared and examined histologically and histomorphometrically. Results: All implants were osseointegrated at the time of exposure. Clinically and histologically, no signs of inflammation in the augmented sites were present. The histomorphometric analysis of 44 biopsy specimens revealed 31.8% ± 11.6% newly formed bone for sites augmented with nanocrystalline HA and 34.6% ± 9.2% for nanoporous HA (P = .467). The proportion of remaining bone substitute material was 28.4% ± 18.6% and 30% ± 13%, respectively (P = .453). The proportion of soft tissue within the biopsy specimens was 39.9% ± 11.1% and 35.4% ± 6.8%, respectively (P = .064). No significant differences were found between the area fractions of bone, bone substitute material, and soft tissue concerning the bone substitute material utilized. Conclusion: Within the present study, both synthetic bone substitute materials, nanocrystalline and nanoporous HA, were found to support bone formation in sinus floor elevation and augmentation procedures by osteoconductivity. They were not completely resorbed after 6 months. The amounts of newly formed bone, soft tissue, and bone substitute material remnants were found to be similar, indicating that both materials are likewise suitable for sinus floor elevation and augmentation procedures. Keywords: bone substitutes, hydroxyapatite, nanocrystalline, nanoporous, sinus floor augmentation