We examined the impact of spinal cord injury to a depth of 0.5 mm at L1-L2 (upper lumbar cord injury) and in L6-S1 (lower cord injury) in Wistar rats. Upper lumbar cord injury resulted in the disappearance of the motor evoked potential (MEP) of the gastrocnemius muscle during transcranial magnetic stimulation, while the threshold was decreased in rats with lower cord injury. During magnetic stimulation of L4-L5, the M-response threshold was decreased in rats with upper lumbar cord injury, while the amplitude was increased. In lower cord injury, the pattern of H-response recruitment curves differed from that in controls. Our results indicated that MEP and the spinal reflex are influenced not only by upper lumbar cord injury but also by lower cord injury.