Our objective was to evaluate the impact of reimplantation techniques of the supra-aortic branches in total arch replacement on the rates of permanent neurological deficit (PND) and survival. We identified patients enrolled in the ARCH registry who underwent total arch replacement between 2000 and 2015 with either en bloc or separate reimplantation of the supra-aortic branches. A total of 3345 patients were included in the present analysis. From this cohort, 686 patients underwent en bloc and 2659 patients had separate reimplantation of the supra-aortic branches. Propensity score analysis identified 461 matched patient pairs. In the matched cohort, there were no differences regarding the mortality rate (15.6% vs 15.7%, P = 0.710) or PND (9.2% vs 12.1%, P = 0.231). Although separate reimplantation of the supra-aortic branches was not associated with an increased mortality rate on multivariable logistic regression, it increased the risk of PND [odds ratio (OR) 1.56, 95% confidence interval (CI) 1.06-2.29; P = 0.023]. Propensity-adjusted regression confirmed these findings and found a similar risk for PND with separate reimplantation of the supra-aortic branches (OR 1.50, 95% CI 1.01-2.23; P = 0.047), although this significance was not found with conditional logistic regression (P = 0.20). No significant differences between survival were seen between the 2 matched cohorts (stratified log rank P = 0.35). Separate reimplantation of the supra-aortic branches in total arch replacement is a significant predictor of stroke in the overall group, although comparable stroke rates were observed in the matched cohort. The current trend towards separate reimplantation of supra-aortic branches may expose certain subgroups of patients to an increased risk of stroke, e.g. those with a high atherosclerotic burden.