Background: Mesenchymal stem cells are one type of adult stem cells, which are able to give rise to mesodermal origin tissues. The application of mesenchymal stem cells for tissue and organ regeneration offer advantages because of the relative ease of collection and their potential to differentiate to 3 cell lineages. Objectives: This research was designed to study and evaluate the effect of mesenchymal stem cells on the repair of bone defects in Wistar rat models and to compare autologous and non-autologous cell transplantation in repairing bone defects. Methods: The mesenchymal stem cells were cultured and expanded in MEM medium supplemented with 10% fetal bovine serum (FBS) and 2% penicillin/streptomycin by incubation at 37°C in 5% CO2. Immunocytochemistry analysis was performed using CD44 and fibronectin markers to detect the mesenchymal stem cells. A transcortical defect was created within the distal epiphyses of the femur bone. After 3 days of injury, Brdu-labeled cells were injected at the site of injury. The animals were sacrificed after 4 weeks of transplantation and the femurs with the recipient area were removed and the length, weight, area, density, and biomechanical parameters were evaluated. Results: The obtained results showed that although neither non-autologous nor autologous cell transplantation significantly improved the effect on length and area of the defective femur bone, the mass and bone density of the cell-injected transplanted groups had a significant increase in comparison with the control and sham groups. Conclusion: It seems that cell transplantation could improve these parameters, improving the mean mass, length, area, and density of parameters during the the regeneration process.