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Heterotaxy is considered a risk factor for poor outcomes after the Fontan operation. However, long-term data to support this notion are lacking. The aims of this study were to ascertain the long-term outcomes of patients with heterotaxy after hospital discharge after Fontan completion and to compare these outcomes with those of a contemporary nonheterotaxy cohort. A binational Fontan registry (n = 1540) was analyzed to identify patients with heterotaxy and compare them with patients without heterotaxy. The primary composite end point was Fontan failure, encompassing death, heart transplantation, Fontan takedown or conversion, protein-losing enteropathy, plastic bronchitis, or New York Heart Association functional class III or IV. A total of 109 patients with heterotaxy were identified and they were compared with 1431 nonheterotaxy patients after Fontan completion. There was no difference in unadjusted 15-year freedom from Fontan failure (heterotaxy, 78% vs nonheterotaxy, 85%; P =.2). Patients in the heterotaxy group had a significantly higher cumulative incidence of post-Fontan arrhythmias (P <.001). Propensity-score matching for confounders yielded 73 patients with heterotaxy matched with 439 patients without heterotaxy, in whom 15-year freedom from Fontan failure was also not different (heterotaxy, 76% vs nonheterotaxy, 81%; P =.2). There was no difference in 15-year freedom from Fontan failure in patients with right vs left isomerism (right isomerism, 80% vs left isomerism, 76%; P =.7). Although heterotaxy may complicate the pre-Fontan course, once the Fontan procedure is successfully completed, heterotaxy does not appear to be an important risk factor for Fontan failure. Patients with heterotaxy are at a higher risk of post-Fontan arrhythmias compared with patients without heterotaxy. [ABSTRACT FROM AUTHOR]