Introduction: Evidence suggests the high capability of non-invasive assessment of the End-tidal carbondioxide (ETCO2) in predicting changes in arterial carbon dioxide pressure (PCO2) following major surgeries in children. We aimed to compare EtCO2 values measured by capnography with mainstream device and EtCO2 values assessed by arterial blood gas analysis before and after cardiopulmonary bypass pumping in cyanotic children. Methods: This cross-sectional study was performed on 32 children aged less than 12 years with ASA II suffering cyanotic heart diseases and undergoing elective cardiopulmonary bypass pumping. Arterial blood sample was prepared through arterial line before and after pumping and arterial blood gas (ABG)was analyzed. Simultaneously, the value of EtCO2 was measured by capnography with mainstream device. Results: A significant direct relationship was found between the changes in ETCO2 and arterialPCO2 (r = 0.529, P = 0.029) postoperatively. According to significant linear association between postoperative change in ETCO2 and arterial PCO2, we revealed a new linear formula between the two indices: ΔPCO2 = 0.89× ETCO2-0.54. The association between arterial PCO2 and ETCO2 remained significant adjusted for gender, age, and body weight. Conclusion: the value of ETCO2 can reliability estimate postoperative changes in arterial PCO2 in cyanotic children undergoing cardiopulmonary bypass pumping.