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To assess the relationship that shunt size, blood gases, and radiologic findings has on respiratory function in infants with univentricular heart physiology.Cardiac catheter laboratory at Rikshospitalet University Hospital, Norway.Fifteen infants with univentricular heart physiology admitted for cardiac catheterization.Lung function was measured by a fixed-orifice differential pressure flow sensor and mainstream volumetric capnography in 15 infants with univentricular heart arrangements during routine invasive assessment before the bidirectional cavopulmonary connection. Blood gases were measured from the indwelling catheters. Chest radiographs were assessed for heart size and pulmonary vasculature. Shunt size was assessed angiographically.Respiratory compliance was reduced in patients with a large surgical systemic-pulmonary arterial shunt (r = −0.67, r2 = 0.45, p = 0.03). Respiratory resistance was higher with increased heart size (r = 0.72, r2 = 0.52, p = 0.004). There was no association between arterial and end-tidal CO2 values. The arterial to end-tidal CO2 difference had an inverse relationship with the pulmonary to systemic shunt ratio (r = −0.38, r2 = 0.14, p = 0.015).A large surgical shunt size is related to stiffer lungs and a large heart is associated with a higher respiratory resistance. During mechanical ventilation of patients with univentricular heart physiology the end-tidal CO2 may be an unreliable substitute for arterial CO2 before the bidirectional cavopulmonary connection. We found a relationship between a decreased pulmonary to systemic shunt ratio and an increased arterial to end-tidal CO2 difference. This may indicate that a reason for the unreliability of end-tidal CO2 is an impaired gas exchange partially due to pulmonary hypoperfusion.