Stem cell-based bone tissue engineering has been recognized as a new strategy for maxillary sinus floor elevation. More rapid bone formation may enhance this technique when simultaneous dental implant placement is desired. Adipose tissue-derived stem cells (ADSCs) and bone marrow stem cells (BMSCs) are the most well-characterized cell sources for bone regeneration, but comparative studies on the osteogenic potential of these cells have yielded conflicting conclusions. This study aimed to compare the rapid bone formation capacity of ADSCs and BMSCs in a canine sinus floor augmentation model. In in vitro studies, BMSCs had a higher proliferative ability and greater osteogenic differentiation potential at both the mRNA and protein levels. When GFP-labeled cells on calcium phosphate cement (CPC) scaffolds were implanted subcutaneously into nude mice, both ADSCs and BMSCs survived for 4 wks, but only BMSCs formed new bone. Furthermore, according to sequential fluorescence labeling results for the canine sinus, BMSCs promoted rapid and greater bone regeneration during the entire observation period. In contrast, obvious mineralization was detected starting from 3 wks after implantation in the ADSC group. These results suggest that BMSCs might be more useful than ADSCs for rapid bone regeneration for sinus augmentation with simultaneous implant placement.