Increased pulmonary dead space fraction (VD/VT) has been associated with prolonged mechanical ventilation after surgery for congenital heart disease. The association of VD/VT with clinical outcomes in neonates undergoing stage 1 palliation for single ventricle congenital heart disease has not been reported. We describe changes in VD/VT, differences in VD/VT based on shunt type (right ventricle to pulmonary artery conduit vs modified Blalock-Taussing shunt) and association of VD/VT with postoperative outcomes in patients undergoing stage 1 palliation.Retrospective chart review for demographic, hemodynamics, outcome information, and VD/VT values were collected at 6-hour intervals during the first 48 postoperative hours in neonates undergoing stage 1 palliation. VD/VT was calculated using mixed expired CO2 (PeCO2) obtained from capnography and paired arterial blood gas CO2 values.Cardiac ICU in a tertiary care pediatric hospital.Newborns with single ventricle congenital heart disease undergoing stage 1 palliation during 2003-2004.Of the 51 patients, 31 had right ventricle to pulmonary artery and 20 had Blalock-Taussing shunt. Although VD/VT was lower in the Blalock-Taussing shunt group over all time points (p = 0.02), maximal VD/VT on day 1 (0.49 ± 0.07) and on day 2 (0.46 ± 0.08) were not different between the shunt groups. VD/VT decreased significantly over time in both shunt groups (p = 0.001 for right ventricle to pulmonary artery; p < 0.001 for Blalock-Taussing shunt). Higher maximal VD/VT during first 48 postoperative hours was independently associated with fewer ventilator (β = -26.6; p = 0.035) and hospital-free days in the first month after stage 1 palliation (β = -40.4; p = 0.002) after adjusting for potential confounders in a multivariable linear regression model.Increased pulmonary dead space exists early after stage 1 palliation operation for single ventricle congenital heart disease. Higher VD/VT during the first 48 postoperative hours was associated with longer duration of ventilation and hospital LOS and may be a useful marker of postoperative outcomes in this population.