We have examined the conduction pathways of motor evoked potentials (MEPs) elicited by transcranial magnetic stimulation, and their correlation with locomotor function in rats. MEPs were concomitantly recorded from the spinal cord (sMEPs) and the limb muscles (mMEPs) before and after various spinal tract ablations. Motor function was also examined using an inclined plane test. sMEPs were composed of four negative peaks (N1-N4) and mMEPs of high-voltage, biphasic waves. Ventral funiculus transection reduced the N1-N3 peaks and abolished mMEPs. Contrarily, dorsal funiculus transection including the pyramidal tract did not alter these MEPs. Motor performance on an inclined plane was worse after ventral funiculus transection than after other transections. These findings indicate that, in rats, the N1-N3 peaks of magnetic sMEPs conduct ventral funiculus activity, and that magnetic mMEPs mainly reflect extrapyramidal activities and are correlated with locomotor function.