A case of an unusual iatrogenic aortic dissection is reported. A 77-year-old male patient in shock status due to acute type A aortic dissection underwent emergency surgery. Systemic perfusion was started via the femoral artery, but another dissection appeared in the descending aorta detected by transoesophageal echocardiography. However, the flap was unusually thin, and there was no change in the pre-existing thrombosed false lumen. These findings suggested subintimal development of dissection. After systemic perfusion was promptly switched to antegrade perfusion, the new dissection could no longer be detected. Since there was no malperfusion or aortic rupture, the ascending aorta was repaired. His postoperative course was uneventful, and there were no significant complications. Unless the aorta is carefully observed at the right time during the operation, such vanishing aortic dissection may be missed and potentially result in ‘organ damage of unknown cause’.