Objective: To assess endothelial dysfunction and the risk for coronary atherosclerosis in children with irreversible pulmonary hypertension due to congenital heart disease (CHD). Methods: The study included 18 cyanotic patients (the mean age was 12.28 3.26 years) who developed irreversible pulmonary hypertension due to cyanotic and acyanotic CHDs, and 18 control patients (the mean age was 11.78 3.00 years). Study groups were compared for flow-mediated dilatation (FMD), carotid intima media thickness (CIMT) and atherosclerotic risk factors. Results: Compared to the control group, the mean FMD was significantly reduced in the cyanotic group (5.26 2.42% and 9.48 2.60%, respectively; P-value < 0.001). No significant difference was observed between the groups in CIMT (0.41 0.08 mm and 0.39 0.06 mm, respectively; P-value = 0.299). The levels of total cholesterol, low-density lipoprotein-cholesterol and very low-density lipoprotein-cholesterol were statistically significantly lower compared tothe control group (P-value = 0.001, 0.006 and 0.014, respectively), whereas no statistically significant difference was found in the levels of high-density lipoprotein-cholesterol and triglycerides (P-value = 0.113 and 0.975, respectively). Conclusions: Systemic endothelial dysfunction in children with irreversible pulmonary hypertension due to CHD was noted but there was no increased risk for atherosclerosis.