Congenital heart disease (CHD) is one of the most specific and yet challenging fields of heart surgery. Apart from the known clinical approaches, including surgery, a significant scale of regenerative therapeutic options is available, which increase the number of cardiomyocytes and restore cardiac function. Although it has been revealed in recent years that mitochondrial transplantation can be used as a promising treatment option in this disease group, there is no clinical evidence for the significance of mitochondrial function in myocardial tissue of patients with CHD regarding cardiac surgery. In this study, mitochondrial morphology and function, myocardial fibrosis, and myocyte atypia were evaluated in myocardial biopsy tissue of pediatric patients with cyanotic and acyanotic CHD, five from each group. After histopathological evaluation of myocardial tissue specimens, mitochondrial morphology and network were analyzed by immunofluorescence staining using an anti-Tom20 antibody, electron transport chain complexes of myocardium were examined by cytochrome c oxidase/succinate dehydrogenase staining, and the amount of ATP was measured by bioluminescence assay. In addition, cardiac markers have been tested to be reviewed as a potential indicator for postoperative follow-up. Myocyte atypia and fibrosis were classified on a scale of 1 to 4. In this study, unlike patients with acyanotic CHD, alterations in mitochondrial network and reduction in ATP production were detected in all pediatric patients with cyanotic CHD. A statistically significant correlation was also determined between mitochondrial dysfunction and cardiac markers. These findings may be assumed as a promising pathway for evaluating the relationship between mitochondrial dysfunction and cyanotic CHD.