Background: Children with ß-thalassemia major are at higher risk for myocardial dysfunction that adversely affects their quality of life. Cardiac biomarkers are valuable tool for assessment of such children. Our aim was to assess heart fatty acid-binding protein (H-FABP) versus B-type natriuretic peptide (BNP) in thalassemia patients as biomarkers of myocardial dysfunction. Methods: This controlled study involved 35 children with ß-thalassemia major and 35 healthy children. Clinical assessment, echocardiography, serum ferritin, BNP and H-FABP were done. Results: H-FABP and BNP were higher in thalassemia than healthy children. Left ventricular dimension and pulmonary pressure were significantly higher and ejection fraction was significantly lower in thalassemia patients. H-FABP has positive correlation with BNP, left ventricular dimension, pulmonary pressure, serum ferritin and the duration of blood transfusion. Conclusion: Elevated H-FABP is associated with myocardial dysfunction in otherwise asymptomatic thalassemia patients.