The object of our study was to analyze the results of bidirectional cavopulmonary anastomosis (BCPA) and modified Fontan operations (MFO) in patients with a functionally single ventricle and heterotaxy syndrome and to reveal risk factors for these surgical interventions. During 1983-2010, 681 patients underwent BCPA or MFO. Thirty-nine had heterotaxy syndrome. The median follow-up period after BCPA and MFO was nine and 1.5 years, respectively. Risk factors for lethal outcomes were determined by logistic regression analysis. Hospital mortality after BCPA and MFO was 7.9% and 12.5%, respectively and did not significantly differ from patients without heterotaxy. The most frequent hospital complications were heart failure, pleural effusions, and arrhythmias. Late mortality after BCPA and MFO was 8.7% and did not significantly differ from patients without heterotaxy. Late deaths were caused by congestive heart failure or pulmonary thromboembolism. The main non-lethal complication was arrhythmia. Patients have significantly improved their functional class at follow-up. The independent risk factor for lethal outcomes after BCPA and MFO was preoperative regurgitation at atrioventricular valves (P=0.012). BCPA and MFO in patients with a functionally single ventricle and heterotaxy syndrome allow to significantly improves their quality of life. Preoperative regurgitation at atrioventricular valves worsens surgical results.