To determine the usefulness of magnetic motor-evoked potentials (MMEPs) for assessing the integrity of the cervical, thoracic, and thoracolumbar spinal cord in horses with bilateral hind limb ataxia. 9 horses and 1 donkey with bilateral hind limb ataxia of various degrees. The motor cortex was stimulated magnetically, and MMEPs were recorded bilaterally from the extensor carpi radialis and cranial tibial muscles. In 5 horses and 1 donkey, MMEPs with normal onset latencies and peak-to-peak amplitude were recorded from the extensor carpi radialis muscles, whereas abnormal onset latencies and peak-to-peak amplitudes were recorded from the cranial tibial muscles. In these animals, a spinal cord lesion in the thoracic or thoracolumbar segments was suspected. In 4 horses, onset latencies and peak-to-peak amplitude of MMEPs recorded from the extensor carpi radialis and cranial tibial muscles were abnormal. In these horses, a cervical spinal cord lesion was suspected. Transcranial magnetic stimulation can be considered a valuable diagnostic tool for assessing the integrity of the spinal cord, and MMEPs may be used for differentiating thoracic or thoracolumbar spinal cord lesions from mild cervical spinal cord lesions that cause ataxia in the hind limbs only.