Background. Heterotaxy is considered a risk factor for adverse events at all stages in the pre-Fontan pathway, and Fontan outcomes are expected to be worse in patients with heterotaxy. The aim of this study was to review existing literature reporting outcomes of the Fontan operation systematically in patients with heterotaxy.Methods. A systematic review and meta-analysis was performed to identify and synthesize early mortality and medium-and long-term survival in heterotaxy patients after the Fontan procedure. Subsequent outcome analyses were stratified by study period era, cohort size, and proportion of right versus left atrial isomerism to explore predictors of outcome.Results. A total of 21 studies were included for analysis, which were composed of 848 post-Fontan heterotaxy patients. Early mortality varied between 1% and 30% with a weighted event rate of 14% (95% confidence interval [CI], 10%-19%). Survival at 1, 5, and 10 years was 86% (95% CI, 79%-91%), 80% (95% CI, 71%-87%), and 74% (95% CI, 59%-85%), respectively. Stratification by study period highlighted that studies with a median study period year of 1995 or later had similar early mortality and 1-and 5-year survival, but superior 10-year survival (P [ .02) compared with earlier studies. Stratification by cohort size and right versus left atrial isomerism did not reveal subgroup differences.Conclusions. Compared with existing literature, in patients with heterotaxy, early mortality after Fontan is higher than for the overall Fontan population. Long-term survival is comparable to the overall Fontan cohort. When heterotaxy patients are successfully transitioned to Fontan, subsequent survival is acceptable and predictable. Long-term follow-up is lacking.