Objectives: The objective of the present study is to investigate the role of cystatin C as an early marker of glomerular dysfunction in thalassemia major. Study Design: Cross sectional comparative study. Setting: Department of Biochemistry Post Graduate Medical institute with the Thalassemia Center in Sir Ganga Ram Hospital Lahore. Period: July 2017 and July 2018. Material & Methods: This study examined 90 male children all between the ages of 5-11, using non probability sampling techniques. The children were grouped as 21 healthy male children as control group I and 69 diagnosed male thalassemia major children further subdivided on the basis of serum ferritin level as group II, serum ferritin level <2500ng/ml, group III, serum ferritin level 2500-5000ng/ml and group IV serum ferritin level >5000ng/ml respectively. Individuals with hereditary renal diseases, on steroid therapy, or other co-morbid renal diseases were excluded from the study. Complete blood analysis, serum ferritin, creatinine and cystatin C were measured by Micro lab 300 and solid phase enzyme linked immune sorbent assay (ELISA) respectively. The results were compared by using SPSS version 20. Results: Group I: n=21 healthy children with ferritin between normal range 105.33 ± 30.03, serum creatinine 0.41 ± 0.05, serum cystatin C 0.57 ± 0.14. eGFR-creatinine 133.38±7.63, eGFR-cystatin C 122.9±17.63. Group II: n=20 (β-TM with ferritin <2500ng/ml). Mean ferritin was 1997.5±300.68 ng/ml (P<0.001), creatinine was 0.43± 0.05, serum cystatin C 0.66 ± 0.05 (P<0.05). eGFR-creatinine 121.45±4.89 P<0.05, eGFR-cystatin C 105.15±6.49 P<0.001. Group III: n= 25 (β-TM with ferritin 2500-5000 ng/ml). Mean ferritin level was 3850.0± 718.18 ng /ml (P<0.001), creatinine was 0.5±.07, cystatin C 0.96±0.13 (P<0.001). eGFR-creatinine 103.29±8.26(P<0.001), eGFR-cystatin C 75.75±10.67 (P<0.001). Group IV: n=24 (β-TM with ferritin >5000 ng/ml). Mean ferritin level was 6311.67±1060.61 ng/ml P value (P<0.001), creatinine was 0.57 ± 0.07, cystatin C 1.11 ± 0.09 (P<0.001). eGFR-creatinine 94.42±8.69 (P<0.001), eGFR cystatin C 64.67±4.23(P<0.001). Conclusion: A highly significant positive relation was found between serum ferritin-cystatin C as compared to creatinine among the study groups II, III and IV and significant inverse relationship between cystatin C and eGFR that concluded cystatin C as an early marker of glomerular dysfunction than creatinine in thalassaemia major children.