Background: Although advancements have been made in the management of thalassemic patients, many unrecognized complications have emerged, such as renal abnormalities. Aim: To measure serum levels of cystatin-C and β-2 microglobulin in children with betathalassemia major (β-TM) and investigate their significance as early markers of glomerular and tubular dysfunctions. Subjects and methods: The study was performed on 70 children with (β-TM) and 20 apparently healthy children matched for age and sex as a control group. For all the enrolled children, a comprehensive medical history was obtained and complete physical examination was performed, blood urea, serum creatinine, serum ferritin, estimated glomerular filtration rate (eGFR) by Schwartz formula and creatinine clearance, albumin/creatinine ratio in urine, serum cystatin-C levels and β-2 microglobulin were measured. Results: Thalassemic children had significantly higher cystatin-C and β-2 microglobulin levels compared with control. In addition, serum cystatin-C and β-2 microglobulin were positively correlated with urea, creatinine, serum ferritin, albumin/creatinine ratio, duration of chelation therapy and frequency of blood transfusion/year and negatively correlated with creatinine clearance, hemoglobin, and eGFR. Our data demonstrated that cystatin-C and β-2 microglobulin had higher sensitivity and specificity (91.4%, 90.0%, and 85.7%, 100%, respectively) than serum creatinine and creatinine clearance (83.0%, 100% and 81.4%, 100%, respectively) for small changes in GFR. Conclusion: Cystatin-C and β-2 microglobulin are specific and sensitive early biomarkers for monitoring glomerular and tubular dysfunction in children with β-TM.