Pulse oximetry overestimates arterial oxygen saturation (SaO2 ) at less than 90% saturation in cyanotic children. The Masimo Blue sensor (Masimo Corp., Irvine, CA) is a pulse oximetry sensor developed for use in children with cyanosis. However, there remains a lack of research in actual clinical practice. We evaluated the intraoperative performance of three different pulse oximeters to measure oxyhemoglobin saturation (SpO2 ) at low saturations in pediatric patients with cyanotic heart disease and the influence of clinical variables (SaO2 , hemoglobin concentration, perfusion index, and weight) on the accuracy of the sensors. This prospective observational study compared SpO2 measured using three pulse oximeters (Masimo Blue [Masimo Corp., Irvine, CA]; Masimo LNCS, and Nellcor [Medtronic, Dublin, Ireland]) at selected SaO2 ranges (≥85%, 75%-84%, 60%-74%, and<60%). Accuracy was evaluated according to bias and Bland-Altman analysis with appropriate correction for multiple measurements. Relationships between bias and clinical variables were assessed using a generalized estimating equation. Two hundred and fifty-eight samples were analyzed. The mean overall bias (limits of agreement) of Masimo Blue, Masimo LNCS, and Nellcor sensor was -5.3 (-20.9 to 10.3%), -7.4 (-21.9 to 7.1%), and -7.4 (-22.5 to 15.1%), respectively. However, there was no difference in bias among the three sensors at SaO2 <60%. Generalized estimating equation showed that SaO2 value was associated with bias of all sensors. Perfusion index affected the bias of Blue sensor and LNCS sensor, and patients' weight was associated with bias of Nellcor sensor. Masimo blue sensor demonstrated overall lower bias compared to the other two sensors. However, the accuracy of all sensors was similarly poor at SaO2 less than 60%. Bias was influenced by SaO2 , perfusion index, and body weight.