Background: Failure to thrive is a common problem in children with congenital heart disease (CHD). Resting energy expenditure (REE) in cyanotic and noncyanotic children with CHD before and after open heart surgery has hardly been investigated. Methods: Twenty-nine children younger than 3 years of age with CHD (14 cyanotic and 15 noncyanotic CHD) who were referred for open heart surgery were enrolled. Data on dietary intake, anthropometric measurements, and indirect calorimetry parameters were measured 24 hours before the surgery, (day -1), and on day 5 after surgery. The measured REE was compared with the Schofield and World Health Organization (WHO) REE prediction equations. Results: The mean ± SD measured REE was similar in the cyanotic and noncyanotic children before and after surgery (before surgery: 57 ± 13 and 58 ± 9 kcal/kg per day, respectively; 5 days after surgery: 59 ±10 and 62 ± 10 kcal/kg per day, respectively). Oxygen consumption (Vo2) and carbon dioxide production (Vco2) did not change significantly before and after surgery and were similar in both groups. The measured REE for all children on day -1 and day 5 was similar to the calculated REE using the Schofield equation but was significantly different from the calculated REE using the WHO equation (p < .01). Conclusions: Significant changes in REE, Vco2, and Vo2 were not observed before and 5 days after open heart surgery in children with CHD. These parameters (REE, Vco2, and Vo2) were also similar in children with cyanotic versus noncyanotic CHD. The Schofield equation is more accurate than the WHO equation in predicting energy needs of children with CHD, but measurement of REE is preferred over calculation of REE.