Purpose: The aim of this study was to evaluate bone healing after the use of a xenograft scaffold enriched with bone marrow mesenchymal stem cells (BM-MSCs), an autogenous bone graft, or the scaffold without BM-MSCs. Materials and Methods: Eighteen rabbits were used for this study; bilateral 12-mm-diameter defects were created in the animals' parietal bones. The bilateral defects were filled with a xenograft enriched with BM-MSCs (test group [TG]), with autogenous bone graft (positive control group [PCG]), or with a xenograft alone (negative control group [NCG]). In all groups, randomly, one defect was covered with a collagen membrane. The rabbits were sacrificed 8 weeks after surgery, and their parietal bones were harvested and analyzed histomorphometrically. Results: Within the PCG and the NCG, the defects covered with the barrier membrane showed better bone healing. In the TG, the defects covered with the barrier membrane did not show better bone healing (intragroup comparisons by Wilcoxon and Friedman tests for paired data). TG showed percentage of mineralized tissue (MT) of 56.03% ± 3.49% with membrane and 57.71% ± 5.31% without membrane. PCG showed MT of 55.13% ± 4.83% and 49.69% ± 3.81% with and without membrane, respectively, and NCG showed MT of 26.77% ± 7.29% and 19.67% ± 2.66% with and without membrane, respectively. Conclusion: Both autogenous bone graft and a xenograft enriched with BM-MSCs were equally effective for bone reconstruction and better than the xenograft alone. The use of a barrier membrane seemed to have a synergistic effect on bone healing in PCG and NCG but not in TG. Keywords: bone marrow, bone repair, cell transplantation, osteogenesis, stem cells