The myocardial uptake of substrates in children has only been investigated on a small scale. The purpose of this study was to define myocardial substrate uptake in relation to the arterial supply of substrates, age, growth and oxygen saturation. Thirty patients with congenital heart disease, aged 3 months to 16 years, were studied during cardiac catheterization. Arterial and coronary sinus blood was analyzed for the major fuel metabolites and amino acids. The uptake of all major substrates correlated significantly with the arterial supply: free fatty acids (r = 0.52, p = 0.004), beta-hydroxybutyrate (r = 0.74, p < 0.0001), lactate (r = 0.70, p < 0.0001) and glucose (r = 0.48, p = 0.01). Free fatty acids were the dominant substrate, irrespective of age, growth and saturation. With age, there was an increase in the uptake of lactate (r = 0.61, p = 0.0004) and a decrease in the uptake of beta-hydroxybutyrate (r =-0.41, p = 0.02). In multivariate analyses, these changes were explained by the arterial supply of the substrates, while age per se did not contribute significantly. The uptake of myocardial metabolites correlated with the arterial supply. Free fatty acids were the dominant substrate at all ages. The uptake of lactate and beta-hydroxybutyrate, although varying with age, was also determined by the arterial supply.