Sickle cell anaemia (SCA) is a multisystem disorder affecting nearly all body organs including the kidneys. Estimation of the glomerular filtration rate (GFR) is the best clinical tool for assessing renal function. Creatinine based estimation is widely used in clinical practice despite some shortcomings. A relatively newer marker, cystatitin C is considered to be superior to creatinine. This was a cross-sectional study that employed a comparative design to determine the estimated GFR of children with SCA using cystatin C and creatinine in order to ascertain the biomarker that more suitably detects early onset of renal impairment. The cystatin C was analyzed by an enzyme-linked immunosorbent assay and GFR was estimated using the Filler formula. While creatinine was determined by the kinetic modification of the Jaffe procedure and the GFR was estimated using updated Schwartz formula. Two hundred children with SCA were recruited from the sickle clinic of the Consultant Outpatient department of the University of Benin Teaching Hospital (UBTH) and the Sickle Cell Centre of Central hospital Benin, as the study subjects. The same number of apparently healthy school children, matched for age and sex with the SCA patients, was recruited from a nursery, primary and secondary school as controls. The data was analyzed using International Business Machine Statistical Package for Scientific Solutions (IBM – SPSS) software version 21. Of the 200 children with sickle cell anaemia (SCA), 111 (55.5%) were males and 89 (44.5%) were females giving a male to female ratio of 1.3: 1. A similar ratio was found in the controls.