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Objective: Mesenchymal stem cells (MSCs) have shown promise in potentially repairing injured spinal cord. These and similar cell types are being tested clinically, but the understanding about delivering method and subsequent results is lacking. This study was designed to compare the MSCs engraftment results after intralesional, intracisternal, or intravenous injection in a rat with spinal cord injury (SCI). Methods: A total of 48 male Sprague-Dawley rats (300-350 g in size) were used with 12 in each group. Allogenic MSCs were cultured from human bone marrow aspirates. The SCI was induced using an NYU (New York University) impactor and MSCs were transplanted 1 week after the SCI. Behavioral testing was performed weekly for 6 weeks. The recipients were analyzed histologically to evaluate the extent of cell delivery and survival at the injury site. Results: All three experimental groups showed better behavioral recovery compared with the control group since 6 weeks after stem cell injection (p<0.05). The intracisternal injection group showed the best functional improvement (p<0.05). The intralesional injection group showed the best engraftment until 4 weeks after stem cell injection (p<0.05). A number of the injected MSCs were trapped in the spleen in the intravenous injection group. Conclusion: Transplantation of stem cells by a variety of routes can deliver cells with the potential to repair injured spinal cord. Intracisternal injection can easily be translated to patients after some modifications, thus accelerating clinical application of cell therapies.