Objective: The present study aims to identify the role of inflammatory markers such as C-reactive protein, interleukin-6, and fractalkine in CHD-associated pulmonary hypertension in children. Methods: This is a prospective review of 37 children with CHD-related pulmonary hypertension, 21 children with congenital heart defects, and 22 healthy children. Results: Serum C-reactive protein and interleukin-6 levels were significantly higher in the children with CHD-related pulmonary hypertension (respectively, p= 0.049 and 0.026). Serum C-reactive protein concentrations correlated negatively with ejection fraction (r =-0.609, p= 0.001) and fractional shortening (r =-0.452, p= 0.007) in the pulmonary hypertension group. Serum fractalkine concentrations correlated negatively with ejection fraction (r=-0.522, p= 0.002) and fractional shortening (r =-0.395, p= 0.021) in the children with pulmonary hypertension. Serum interleukin-6 concentrations also correlated negatively with Qs (r=-0.572, p= 0.021), positively with Rs (r = 0.774, p= 0.001), and positively with pulmonary wedge pressure (r = 0.796, p= 0.006) in the pulmonary hypertension group. A cut-off value of 2.2 IU/ L for C-reactive protein was able to predict pulmonary hypertension with 77.5% sensitivity and 77.5% specificity. When the cut-off point for interleukin-6 concentration was 57.5 pg/ ml, pulmonary hypertension could be predicted with 80% sensitivity and 75% specificity. Conclusion: Inflammation is associated with the pathophysiology of pulmonary hypertension. The inflammatory markers C-reactive protein and interleukin-6 may have a role in the clinical evaluation of paediatric pulmonary hypertension related to CHDs.