Several effective strategies for spinal cord protection have been advocated in descending and thoracoabdominal aortic repairs. The segmental clamp technique has been known as a useful adjunct to shorten the duration of spinal cord ischemia. However, we experienced two cases of spinal cord malperfusion during segmental aortic clamping in descending aortic repair for chronic type B aortic dissection. In these patients, the intercostal arteries including the Adamkiewicz artery had originated from the false lumen. In one patient, spinal cord ischemia was initially detected as decreased motor-evoked potentials. Transesophageal echocardiography simultaneously revealed blood flow congestion in the false lumen during segmental aortic clamping and spinal cord ischemia had developed due to malperfusion of the intercostal arteries branching from the false lumen. Segmental clamping in patients with aortic dissection may not always be useful for shortening the duration of spinal cord ischemia. Transesophageal echocardiography as well as motor-evoked potentials is a useful modality for obtaining the details of intraoperative blood flow in dissecting lumens and malperfusion of the intercostal arteries related to spinal cord injury.