BACKGROUND: The arterial to end-tidal carbon dioxide tension difference(Pa-ETCO2) can be increased in patients with congenital heart disease(CHD) and, therefore, end-tidal carbon dioxide tension(PETCO2) does not accurately approximates arterial carbon dioxide tension(PaCO2). The purpose of this study was to evaluate the stability of the Pa-ETCO2 in pediatric patients with congenital heart disease undergoing open heart surgery. METHODS: Forty three children with CHD were studied: twenty two were acyanotic and twenty one were cyanotic. Simultaneous PETCO2 and PaCO2 measurements, as well as pulse rate, blood pressure, pH and arterial oxygen tension(PaO2) were obtained for each patient during four intraoperative events: (1) after induction of anesthesia and before sternotomy, (2) after sternotomy and before cardiopulmonary bypass(CPB), (3) after weaning of CPB, and (4) after closure of sternotomy. RESULTS: The PETCO2 of cyanotic group were lower than that of acyanotic group throughout operation period, and did not change significantly after CPB. Cyanotic children demonstrated a greater Pa-ETCO2 difference before CPB as compared with acyanotic group. In acyanotic group, Pa-ETCO2 difference increased significantly after CPB(P <0.05), whereas it remained unchanged in cyanotic group. CONCLUSIONS: Since cyanotic children had higher Pa-ETCO2 differences intraoperatively and acyanotic children showed an increase in Pa-ETCO2 after CPB, the PETCO2 cannot be the alternative value to estimate reliably the PaCO2 during open heart surgery of pediatric CHD.