Purpose: The aims of this study were to investigate the best two of five common methods of collecting autologous bone (preliminary study [PS]) and to test clinically the effects of autografts harvested using a trephine bur or bone scraper for sinus augmentation surgery (main study [MS]). Materials and Methods: In the PS, five autograft samples from five patients (n = 25) were harvested with a bone scraper, round bur, piezoelectric device, implant bur, and trephine bur and were processed for histomorphometric analysis. In the MS, sinus augmentation was performed on 20 patients using bovine-derived bone substitute and autograft collected with a trephine bur (group A, n = 10) or collected with a bone scraper (group B, n = 10). Narrow implants were also placed. At 6 months, changes in graft volume were evaluated with cone beam computed tomography. The amounts of regenerated bone, residual graft, and osseointegration of the implants were assessed histologically. Results: In the PS, the trephine bur and bone scraper harvested bone chips that were medium to large and more vital than those obtained with the other tools. In the MS, no significant differences were seen between groups in terms of the amount of residual biomaterial, regenerated bone, change in graft volume, and osseointegration. Conclusion: Biologic differences between these two bone particulates may not influence regeneration and implant osseointegration in sinus augmentation when mixed with xenograft bone. Keywords: autograft, bone regeneration, cone beam computed tomography, sinus augmentation, tissue harvesting, xenograft