Clinical evaluation of intracardiac shunts in children is not straightforward. Echocardiography can only diagnose the presence of a shunt but does not estimate the shunt ratio. This can be a critical factor that influences treatment options. In this single-center, prospective, observational, method-comparison study, we validate the ability of a novel monitoring device COstatus to estimate the intracardiac shunt ratio (Qp/Qs) of pulmonary (Qp) to systemic (Qs) blood flow in young children before and after corrective cardiac surgery. The indicator dilution technology COstatus monitor was compared to two other more invasive reference techniques, perivascular ultrasonic flow probes (placed around the pulmonary truncus and ascending aorta) and the oximetric shunt equation (using arterial and venous blood gases). Our study revealed that the COstatus monitor detected intracardiac shunts with high sensitivity and specificity but there was some underestimation of the shunt ratios compared to the reference techniques.