Objectives: The present study was undertaken to identify risk factors for permanent neurological dysfunction (PND) and in-hospital mortality after total aortic arch replacement (TAR) with separate arch vessel grafting using selective cerebral perfusion (SCP) and hypothermic circulatory arrest. Methods: Between 1998 and 2008, we preformed a TAR on 143 consecutive patients in two centers by identical methods. Of these, 19 (13.3%) were emergency operations, and 46 (32.2%) were open stent-graft placements. Statistical analysis was performed to determine risk factors for PND and mortality, and furthermore, the survival rate was analyzed. Results: The in-hospital mortality rate was 4.9%, with chronic renal failure (p = 0.0013, odds ratio 10.0) as a significant risk factor. Nine patients (6.3%) had PND, with significant risk factors identified as (1) the presence of an old cerebral or silent lacunar infarction on preoperative imaging methods ( p = 0.0458, odds ratio 8.0) and (2) duration of SCP ( p = 0.0026, odds ratio 1.036). Long-term survival was the same in patients with or without PND. Conclusion: The enhanced vulnerability of the brain in patients with a pre-existing old cerebral infarction or silent lacunar infarction is reflected by a high incidence of PND. Chronic renal failure had an impact on in-hospital mortality.