Few data exists on the differences in long-term outcome between Mustard and Senning operations. We reviewed available data of all hospital survivors of these operations and assessed risk factors for late death and sinus node dysfunction. Of those patients undergoing the Mustard operation, 60 were hospital survivors (46 simple transposition, 14 complex); of those patients undergoing the Senning operation, 62 were hospital survivors (43 simple, 19 complex). Median duration of follow-up was 16 years (maximum 25 years) for Mustard operation, 11 years (maximum 20 years) for Senning operation. No reoperations were done, except for pacemaker implantation. No differences were found between the two groups with regard to baffle-associated problems, right ventricular failure, sudden death (6% in both groups), and functional status at final follow-up (New York Heart Association class I or II, except for four patients). For patients undergoing the Mustard operation, survival at 16-year follow-up was 91% with simple transposition and 60% with complex transposition (p = 0.027); for both groups of patients undergoing the Senning operation, survival at 16-year follow-up was 78%. Survival in the absence of rhythm disturbance at 16-year follow-up was 18% for Mustard operation and 53% for Senning operation (p < 0.001). In multivariate analysis, significant independent risk factors for late death turned out to be complex transposition (versus simple) and active arrhythmias. The only significant risk factor for the occurrence of sinus node dysfunction was the Mustard operation. We conclude that apart from the difference in the loss of sinus rhythm, no differences were found in the long-term clinical results of the two types of operations.