Heterotaxy syndrome (HS) is a significant determinant of outcome in single ventricle (SV) physiology. Attrition rate and time-related events associated with intestinal malrotation (IM) are, yet, to be determined. We sought to evaluate hospital and interstage outcomes in relation with operative intervention for IM (IMO). Twelve SV/HS patients, who underwent IMO, from January 2004 to December 2016, were studied. Early shunt failure, time to superior cavopulmonary connection (SCPC) and interstage attrition were assessed. Since September 2014, based on a comprehensive standardized protocol, IMO was performed at the time of hospitalization for stage-I palliation (S1P) irrespective of clinical manifestations. Patients were assigned to Group A (n = 8): expectant /symptoms-driven versus Group B (n = 4): protocol-driven. At S1P 7 had systemic-to-pulmonary shunt (SPS), 1 SPS with anomalous pulmonary venous return (APVR) repair (Group A) compared to 2 SPS, 1 SPS with APVR repair and 1 Norwood operation (Group B). Median duration from S1P to IMO was 82 days (range 57–336; Group A) compared to 14 days (range 11–31; Group B); p < 0.05. Median age at IMO was 87 days (range 8–345) [Group A: 99 days (range 68–345) vs Group B: 25 days (range 8–39)] (p < 0.05). Early SPS failure occurred in 25% (2 of 8) for Group A compared to none in Group B (p < 0.05). Hospital mortality following IMO was 25% [Group A: 37.5% (3 of 8) vs Group B: 0; p < 0.05]. Interstage survival was 67% [Group A: 50% (4 of 8) vs Group B: 100%; p < 0.05]. Time to SCPC following S1P was 186 days (range 169–218) for Group A compared to 118 days (range 97–161) (Group B); p < 0.05. Operative intervention for IM in SV/HS is associated with significant interstage attrition and might impact the time to SCPC. SPS is at risk for early failure after IMO. A comprehensive standardized concept can mitigate detrimental implications.