Patients with single ventricle congenital heart disease are at risk of unpredictable protein-losing enteropathy (PLE) after surgical palliation. Based on prior reports of physiologic differences for patients with single morphologic right versus left ventricles, we hypothesized that those with right ventricular morphology would have a higher incidence of PLE. We performed a retrospective review of > 15 million pediatric hospitalizations from the Healthcare Cost and Utilization Project KID 2000–2012 databases for admissions 5–21 years old with ICD-9 codes for hypoplastic left heart syndrome (HLHS) and tricuspid atresia (TA) with and without PLE. Incidence of PLE was compared between those with HLHS and TA. In addition, outcomes and costs were compared between admissions with and without PLE and between HLHS and TA. Of 1623 HLHS admissions, 289 (17.8%) had PLE, and of 926 TA admissions, 58 (5.9%) had PLE (p < 0.001). Admissions with PLE were older compared to those without PLE (12 vs 10 years, p < 0.001) and PLE onset occurred at a younger age for HLHS than TA (11 vs 14 years, p < 0.001). There were no differences in hospital outcomes or costs. Review of this large administrative database suggests a higher incidence of PLE in patients with HLHS and a younger age of onset compared to those with TA. These data suggest that a single systemic right ventricle may be an independent risk factor for developing PLE.