Negative motor evoked potentials after cerebral infarction, indicative of poor recovery of limb motor function, tend to be accompanied by changes in fractional anisotropy values and the cerebral pe-duncle area on the affected side, but the characteristics of these changes have not been reported. This study included 57 cases of cerebral infarction whose motor evoked potentials were tested in the 24 hours after the first inspection for diffusion tensor imaging, in which 29 cases were in the negative group and 28 cases in the positive group. Twenty-nine patients with negative motor evoked potentials were divided into two groups according to fractional anisotropy on the affected side of the cerebral peduncle: a fractional anisotropy < 0.36 group and a fractional anisotropy ≥ 0.36 group. All patients underwent a regular magnetic resonance imaging and a diffusion tensor imaging examina-tion at 1 week, 1, 3, 6 and 12 months after cerebral infarction. The Fugl-Meyer scores of their hemiplegic limbs were tested before the magnetic resonance and diffusion tensor imaging exami-nations. In the negative motor evoked potential group, fractional anisotropy in the affected cerebral peduncle declined progressively, which was most obvious in the first 1–3 months after the onset of cerebral infarction. The areas and area asymmetries of the cerebral peduncle on the affected side were significantly decreased at 6 and 12 months after onset. At 12 months after onset, the area asymmetries of the cerebral peduncle on the affected side were lower than the normal lower limit value of 0.83. Fugl-Meyer scores in the fractional anisotropy ≥ 0.36 group were significantly higher than in the fractional anisotropy < 0.36 group at 3–12 months after onset. The fractional anisotropy of the cerebral peduncle in the positive motor evoked potential group decreased in the first 1 month after onset, and stayed unchanged from 3–12 months; there was no change in the area of the cer-ebral peduncle in the first 1–12 months after cerebral infarction. These findings confirmed that if the fractional anisotropy of the cerebral peduncle on the affected side is < 0.36 and the area asymme-tries < 0.83 in patients with negative motor evoked potential after cerebral infarction, then poor hemiplegic limb motor function recovery may occur.