BACKGROUND: In neonates and infants with congenital cyanotic heart disease, venous blood, rich in CO2 and poor in O2, is mixed with pulmonary venous blood at left heart. As a consequence, any given degree of decreases in SpO2 is accompanied by obligatory increase in PaCO2 - PETCO2 difference. This study was designed to evaluate these relationship in 20 pediatric patients. METHODS: After endotracheal intubation with high dose fentanyl and pancuroniun, PETCO2 was measured by capnometer (side stream, sample gas flow rate of 200 ml/min; sampling site at elbow connector area) and SpO2 probe was attached at toe or finger. Observations were made 4 or 5 times before initiation of CPB. Ventilation was controlled by pressure type ventilator, partial rebreathing circuit at frequency of 25-35 breaths/min, an inspiratory time of 25% with an end-inspiratory pause of 10%, and peak airway pressure of 20 +/- 2 cmH2O. RESULT : Mean values of PaCO2 - PETCO2 difference were increased linely with decreases in SpO2. The regression equation is mean (PaCO2 - PETCO2) (mmHg) = 23.9 0.22 mean SpO2 (r= 0.51, p=0.028) CONCLUSIONS: The relationship between PaCO2 - PETCO2 was found to agree with that predicted by theory confirming that in congenital cyanotic heart patients, PaCO2 increases by 2-5 mmHg for every 10% reduction in SpO2. This relationship may be useful when attemping to estimate PaCO2 from PETCO2 in the management of congenital cyanotic heart patients.