Patients with single ventricle anatomy undergo staged surgical palliation which results in pulmonary and systemic circulations in series with a single systemic pump. Single right ventricular morphology has been found to be an independent risk factor for worse survival. We sought to compare patients with single left (SLV) and single right (SRV) ventricular morphology to identify hemodynamic differences that may contribute to worse survival in patients with a single right ventricular. Single center, retrospective review of invasive hemodynamic data. All patients with single ventricle anatomy who underwent superior cavo-pulmonary anastomosis (Stage 2 palliation) and/or total cavo-pulmonary anastomosis (Stage 3 palliation) from August 1995 through May 2011 were identified. Patients were compared over time, and SLV and SRV patients were compared. Seventy-nine single ventricle patients (56 % SRV) underwent staged palliation and were analyzed. There was no difference in overall mortality (12 % SLV, 11 % SRV). There was no difference in hemodynamics at pre-Stage 2 catheterization between ventricular morphology, but SRV patients had higher ventricular end-diastolic pressure at pre-Stage 3 catheterization (7.6 vs. 6.4 mmHg, p = 0.026). End-diastolic pressure decreased after Stage 2 surgery for SLV patients, but not SRV patients. Intrinsic differences in morphology, function, and response to performing as the systemic ventricle between single right and left ventricles may lead to an elevated ventricular end-diastolic pressure. This could limit passive flow through the pulmonary circuit and coronary perfusion after Stage 3 palliation and potentially lead to poorer long-term performance for SRV patients.