Objectives: Heterotaxy syndrome is a recognized risk factor for surgical cardiac interventions. We evaluated the early- and middle-term results of a surgical intervention for patients with heterotaxy syndrome. Methods: A total of 42 patients with heterotaxy syndrome were enrolled (September 2008 to March 2015). Left and right atrial isomerism were identified in 26% (11 out of 42) and 74% of patients (31 out of 42), respectively. The median age of the patients at the time of surgery was 6.8 months (range: 5 days to 22.3 years). Biventricular repair was completed in 3 patients with left atrial isomerism. Seventeen out of 39 patients who were scheduled for single ventricular repair completed a modified Fontan procedure. Results: The hospital mortality rate was 4.7% (2 out of 42). Another 5 deaths occurred in the remaining survivors following hospital discharge with a follow-up duration of 45.8 ± 23.6 months (range: 13-111 months). The 1-year and 5-year survival rates were 88.1% (37/42) and 83.3% (35/42), respectively. Univariate analysis and multivariate analysis identified pulmonary venous obstruction and atrioventricular valve replacement as additional risk factors for mortality. Conclusions: Right ventricular bypass surgery remains the preferred palliative procedure for patients with heterotaxy syndrome. Based on the current results, the early- and middle-term outcomes are satisfactory.