OBJECTIVE: The authors investigated the changes of cortical sensorimotor activity in functional MRI (fMRI) and functional recovery in spinal cord injury (SCI) patients who had been treated by bone marrow cell transplantation. METHODS: Nineteen patients with SCI were included in this study; ten patients with clinical improvement and nine without. The cortical sensorimotor activations were studied using the proprioceptive stimulation during the fMRI. RESULTS: Diagnostic accuracy of fMRI with neurological improvement was 70.0% and 44.4% for sensitivity and specificity, respectively. Signal activation in the ipsilateral motor cortex in fMRI was commonly observed in the clinically neurological improved group (p-value=0.002). Signal activation in the contralateral temporal lobe and basal ganglia was more commonly found in the neurological unimproved group (p-value<0.001). Signal activation in other locations was not statistically different. CONCLUSION: In patients with SCI, activation patterns of fMRI between patients with neurologic recovery and those without varied. Such plasticity should be considered in evaluating SCI interventions based on behavioral and neurological measurements.