The aim of this study was to investigate the effects of allogeneic bone marrow-derived MSCs (BM-MSCs) transplantation in acute stage of experimentally generated severe spinal cord injury (SCI) in rats at different intervals. Seventy seven Sprague-Dawley rats were used in this study. The bone marrow was harvested from femurs and tibias of the one day-old rats, then processed using the standard methods. SCI was generated with an aneurysm clip after T9-T10 laminectomy. Intraparenchymal transplantation of the stem cell or stem cell diluent was perfomed at 6th hour after injury. The effects of the BM-MSCs were evaluated by clinical, electrophysiological and histopathological examinations on the 1st, 3rd, 7th and 21st day postoperatively. In clinical examination, hematuria rate was significantly low in treatment comparing to control (P=0.003). The survival rate of the 21th day treatment group was significantly higher than the control group. Significant improvement in somatosensory evoked potentials (SEP) was observed on the 3rd and 7th day in treatment group. The histopathological changes were similar in the control and treatment groups at all intervals. In conclusion, intraparenchymal transplantation of BM-MSCs in the acute phase of the SCI provided some benefical effects regarding to hematuria rate, SEP scores and survival rate. The results of this study found as promising for doing further, more detailed studies on the treatments of spinal cord injury by the MSCs.