We conducted a study to evaluate the degree of corticospinal tract (CST) dysfunction associated with diffuse axonal injury (DAI) through analyses of both diffusion-tensor magnetic resonance imaging (DTMRI) and motor-evoked potential (MEP). Using DTMRI and MEP with transcranial magnetic stimulation, we evaluated 138 instances of CST in 52 patients with severe chronic DAI and compared them with the findings in 17 normal volunteers. We determined values of fractional anisotropy (FA) on FA maps obtained with DTMRI of six regions of interest (ROIs) in the CST, consisting of the semioval center, coronal radiation, posterior limb of internal capsule, midbrain, pons and medulla oblongata. The lowest value of %FA for each of the six ROIs in each CST was defined as the minimum %FA, and the lowest magnetic stimulation strength that produced MEP was defined as the minimum threshold for MEP. The mean minimum %FA for CSTs in which MEP could not be obtained even with maximum magnetic stimulation (the MEP- group) was significantly lower than that of CSTs in which MEP could be obtained (the MEP+ group). ROIs with the lowest %FA value were the midbrain in the MEP+ group and the medulla oblongata in the MEP- group. In the MEP+ group, a serial decrease in the minimum %FA value significantly correlated with a serial increase in minimum threshold for MEP. These results show that in patients with chronic DAI, physiological motor dysfunction as revealed by MEP correlates significantly with morphological damage to the CST as detected by DTMRI. This strongly suggests that DTMRI can be a valuable tool for evaluating aberrant motor function and for estimating its severity in DAI.