Abstract OBJECTIVES Heterotaxy is a known risk factor for morbidity and mortality in single ventricle palliation. In this study, we examined our experience with this challenging group of patients. METHODS Records of patients born between 2001 and 2019 with heterotaxy, who needed staged single ventricle palliation were retrospectively analysed. RESULTS A total of 53 patients were included in this study. Thirty-five (66%) patients had a right ventricular dominance, common atrioventricular septal defect was present in 37 (70%) patients. Anomalous pulmonary venous drainage was present in 29 (55%) patients. Forty-six (86%) patients underwent first-stage palliation. Forty-one (77.3%) patients received a bidirectional cavopulmonary connection. Thirty-one (58%) patients received total cavopulmonary connection (TCPC). Overall survival rate was 92% at 1 month, 74% at 1 year and 68% at 10 years. Twelve (22.6%) patients died before second palliation stage. Four (10%) patients died before TCPC. No patient died after TCPC. Independent risk factors for mortality in the multivariate COX regression were a presence of restrictive pulmonary blood flow (HR 3.23; 95% CI 1.02–10.2; P = 0.05) and greater than mild atrioventricular valve regurgitation (HR 3.57; 95% CI 1.27–10.0; P = 0.02). CONCLUSIONS Mortality and morbidity in patients with single ventricle and heterotaxy are high. Restrictive pulmonary blood flow needing early modulation and greater than mild atrioventricular valve regurgitation at presentation are independent risk factors for mortality. Total anomalous pulmonary venous connection was not identified as a risk factor in the current era.