Actuality: Energy changes in the myocardium can be defined range of carnitine and remain poorly understood, relevant is the study of their children with congenital heart disease. The aim of the study was to investigate the levels of carnitine, acylcarnitines and amino acids in children with congenital heart disease. Material and Methods: To study the performance of bioenergy metabolism in children with congenital heart disease were examined 82 children. Conducted an in-depth analysis of the main indicators of carnitine spectrum (HPLC / MS / MS) in patients with congenital heart disease, with severe hemodynamic and without them. Results: violation of carnitine spectrum due to increased levels of acylcarnitines and reduce free carnitine and methionine in circulatory disorders. Conclusions: Indicators carnitine spectrum can be used to assess the bioenergetic metabolism in children with congenital heart disease.