Patients with 1-ventricle (1V) physiology may be at risk for peripheral arterial dysfunction at a young age. To determine whether infants and young children with 1V physiology and hypoxemia have peripheral arterial dysfunction before undergoing the Fontan operation, we measured (1) flow-mediated vasodilation (FMD) in the brachial artery, (2) serum levels of vasoactive mediators endothelin-1 (ET-1) and metabolites of nitric oxide, and (3) arterial stiffness with pulse-wave velocity (PWV) in the aorta. Eighteen patients with 1V physiology before the Fontan procedure and hypoxemia and 19 patients with normoxemia and 2-ventricle (2V) physiology were studied. Measurements were collected during cardiac catheterization. FMD in the brachial artery was the diameter gain after 4.5 minutes of forearm occlusion measured with high-resolution ultrasound and edge-detection software. Nitric oxide and ET-1 levels were measured in venous blood. PWV between the left carotid and femoral arteries was measured using pulse Doppler ultrasound. FMD was lower (2.4 ± 3.7% vs 11.3 ± 6%, p <0.0005) and ET-1 levels were higher (35.5 ± 11.3% vs 24.1 ± 9.7%, p = 0.003) in subjects with 1V physiology versus those with 2V physiology, respectively. There were no differences in nitric oxide levels or PWV. In conclusion, infants and young children with 1V physiology and hypoxemia have blunted FMD and higher ET-1 levels before undergoing the Fontan operation compared with normoxemic subjects with 2V physiology. A further understanding of pathophysiologic mechanisms underlying peripheral arterial dysfunction, including the roles of hypoxemia, low cardiac index, and ET-1, may lead to targeted therapies and improve the long-term survival of patients with 1V physiology.