Electrophysiological methods to detect the degeneration of the upper motor neuron system have not been fully established in patients with amyotrophic lateral sclerosis (ALS). This may be partly because the parallel demonstration of electrophysiology and a corresponding pathological abnormality is insufficient, and because a substantial number of patients with ALS do not exhibit upper motor neuron degeneration. Recently, we encountered 2 patients with ALS who had been examined for abnormal central motor conduction time (CMCT) using transcranial magnetic stimulation within a 20-day period prior to their death. Autopsy revealed that 1 patient had marked pyramidal degeneration with prolonged CMCT; in contrast, the other patient had no obvious pyramidal degeneration and showed normal CMCT. Both the patients with contrasting clinicopathological differences contributed to the identification that the prolongation of CMCT was possibly linked to the degeneration of the corticospinal tract. This report indicates that CMCT is useful for predicting the severity of upper motor neuron degeneration in patients with ALS.