Growth failure is often observed in infants with congenital heart disease (CHD); it is unclear, however, whether growth failure is due to increased total energy expenditure (TEE). An observational study of infants with CHD and surgical intervention within the first 30 days of life and healthy infants of similar age was undertaken. TEE was measured using the doubly labeled water method in 3-month-old infants (n = 15 CHD, 12 healthy) and 12-month-old infants (n = 11 CHD, 12 healthy). Multiple linear regression models were fit to examine the association between health status (CHD vs. healthy) and TEE. The accuracy of equations for calculating TEE was also determined. TEE for CHD infants was not significantly different from healthy infants at 3 and 12 months; TEE in CHD infants was 36.4 kcal/day higher (95 % CI -46.3, 119.2; p = 0.37) and 31.7 kcal/day higher, (95 % CI -71.5, 134.8; p = 0.53) at 3 and 12 months, respectively, compared to healthy infants. The 2002 Dietary Reference Intake (DRI) equation and the 1989 Recommended Dietary Allowance equation over-estimated measured TEE to a lesser extent than CHD specific equations; the 2002 DRI yielded the smallest mean difference between calculated versus measured TEE (difference 79 kcal/day). During the first year of life, TEE of infants with CHD and interventional surgery within the first month of life was not different than age-matched healthy infants. When calculating TEE of =12-month-old infants with CHD who have undergone surgical intervention, the 2002 DRI equation may be used as a starting point for estimating initial clinical energy intake goals.