Purpose: This randomized, controlled study was designed to compare bone formation around microimplants with a sandblasted, acid-etched surface placed at the time of maxillary sinus floor augmentation with a synthetic biphasic calcium phosphate (BCP) or deproteinized bovine bone (DBB). Materials and Methods: Nine completely edentulous patients and two partially edentulous patients (six women, five men) with a mean age of 67 years (range, 50 to 79 years) requiring bilateral sinus augmentation were included in the study. The patients were randomized for augmentation with BCP (test) in one side and DBB (control) in the contralateral side. At the time of augmentation, one microimplant on each side was placed vertically from the top of the alveolar crest, penetrating the residual bone and the grafting material. After 8 months of graft healing, at the time of ordinary implant placement, all 22 microimplants were retrieved with a surrounding bone core for histologic analyses. Results: The bone-to-implant contact in the BCP group was 64.6% ± 9.0%, versus 55.0% ± 16.0% for the DBB group. The difference was not significant. The corresponding values for the area of newly formed bone in the biopsies were 41.1% ± 9.8% and 41.6% ± 14.0% for BCP and DBB, respectively. There were significantly more DBB particles in contact with newly formed bone than BCP particles (87.9 ± 18.2% versus 53.9 ± 26.1%; Wilcoxon rank sum test; P = .007). Conclusion: In this randomized, controlled clinical trial, new bone formation and bone-to-implant contact around microimplants with a sandblasted, acid-etched surface was found to be equivalent between sinuses augmented with BCP or DBB. Significantly more DBB particles than BCP particles were in contact with newly formed bone, but the clinical relevance of this has yet to be established. Keywords: biphasic calcium phosphate, bone substitutes, deproteinized bovine bone, histology, microimplants, sinus floor augmentation