End-tidal CO2 (ET(CO2)) monitoring and transcutaneous (TC) CO2 monitoring were prospectively compared in 53 patients, 1 month to 16 years of age, with congenital heart disease (CHD). There were 32 patients with cyanotic CHD and 21 with acyanotic CHD. The TC-Pa(CO2) difference was 2 +/- 1 mm Hg and the ET-Pa(CO2) difference was 5 +/- 3 mm Hg (P < .0001). The TC-Pa(CO2) difference was < or = 2 mm Hg in 30 of 53 patients and < or = 5 mm Hg in 53 of 53 patients. The ET-Pa(CO2) difference was< or = 2 mm Hg in 9 of 53 patients and < or = 5 mm Hg in 30 of 53 patients (P < .001). No variation in the TC-Pa(CO2) difference was noted based on the type of CHD (acyanotic vs cyanotic) or age. The ET-Pa(CO2) difference was greater in patients with cyanotic versus acyanotic CHD (7 +/- 3 mm Hg vs 4 +/- 2 mm Hg, P < .0001) and in patients < or = 1 year of age versus patients > or = 1 year of age (6 +/- 3 mm Hg vs 4 +/- 2, P = .008). In infants and children with CHD, TC monitoring provides a more accurate estimation of Pa(CO2) than ET monitoring.