Background. Children with congenital heart diseases (CHDs) may have a risk of developing myocardial injury caused by volume and pressure overload. Objective. To evaluate the incidence of myocardial injury in children with cyanotic and acyanotic CHDs using cTnI assay and to correlate it with different hemodynamic parameters. Methods. This study included 80 children with CHDs (40 acyanotic and 40 cyanotic) as well as 40 healthy children (control group). Serum cTnI levels were measured for patients and control. Pulmonary to systemic blood flow (Qp/Qs) and pulmonary to systemic arterial pressure (Pp/Ps) ratios were measured for children with CHDs during cardiac catheterization. Results. Sixty-four out of 80 patients with CHDs had myocardial injury as evidenced by increased cTnI. Serum cTnI was significantly higher in both cyanotic and acyanotic groups compared to control group (p < 0.05). Serum cTnI level significantly correlated with oxygen saturation (SpO2), ejection fraction (EF), Qp/Qs, and Pp/Ps ratios. Conclusion. The incidence of myocardial injury was high in children with CHDs. The use of cTnI for follow-up of children with CHDs may help early detection of myocardial injury and help early management of these cases.