Heterotaxy syndrome (HS) is a complex disorder involving thoracic and abdominal asymmetries. Congenital heart disease is often accompanied by an intestinal rotation abnormality (IRA) that may predispose to bowel ischemia and infarction. There is controversy in the literature whether asymptomatic infants with HS must be screened for IRA and, if present, whether a prophylactic Ladd procedure should be performed. We performed a retrospective chart review of all patients who underwent a Ladd procedure from January 2007 to December 2010 at Stollery Children's Hospital, Edmonton, Canada. Twenty-nine patients underwent a Ladd procedure, 22 without HS but with symptomatic malrotation and 7 with HS and asymptomatic malrotation. Asymptomatic HS patients had a complication rate of 57 % after a prophylactic Ladd procedure compared with a complication rate of 9 % in the symptomatic non-HS population. The management of asymptomatic IRA in patients with HS remains controversial. We suggest that HS patients be screened for IRA and that asymptomatic patients be managed conservatively.