Background Previous studies have reported a high incidence of acute kidney injury (AKI) after thoracic aortic surgery in heterogeneous patient cohorts, including various aortic diseases and the use of deep hypothermic circulatory arrest. Moderate hypothermia with cerebral perfusion makes deep hypothermia nonessential, but can make end organs susceptible to ischemia during circulatory arrest. We investigated the incidence and risk factors of AKI after thoracic aortic surgery with and without moderate hypothermic circulatory arrest for acute dissection. Methods We reviewed the medical records of 98 patients undergoing graft replacement of the thoracic aorta for acute dissection between 2008 and 2011 at a university hospital. Acute kidney injury was defined by RIFLE criteria, which is based on serum creatinine or glomerular filtration rate. Results The mean age was 55 ± 15 years. The surgical procedures, 96% of which were emergencies, involved the ascending aorta (67%), aortic arch (41%), descending aorta (41%), and aortic valve (5%). Moderate hypothermic circulatory arrest was performed in 75%. The overall incidence of AKI was 54%, and 11% of 98 patients required renal replacement therapy. Thirty-day mortality increased with AKI severity (p = 0.002). Independent risk factors for AKI were long cardiopulmonary bypass duration (>180 minutes; odds ratio, 7.50; p = 0.008) and preoperative serum creatinine level (odds ratio, 8.43; p = 0.016). Conclusions Acute kidney injury was common after thoracic aortic surgery for acute dissection with or without moderate hypothermic circulatory arrest and worsened 30-day mortality. Prolonged cardiopulmonary bypass and increased preoperative serum creatinine were independent risk factors for AKI, but moderate hypothermic circulatory arrest was not.