This study was to evaluate the relative applicability of the most commonly used estimation formulas for renal glomerular filtration rate (GFR) of Chinese children with chronic kidney disease (CKD).One hundred CKD patients of less than 17 years old were divided into two groups by sex which was further categorized into five subgroups based on CKD staging according to the "reference" GFR (rGFR) determined by Tc-99m-DTPA renal dynamic imaging. Four GFR markers including serum cystatin C (CysC), β2-microglobulin, creatinine, and blood urea nitrogen were measured.Among all four markers, CysC best reflected the extent of glomerular damages for CKD stage 1. The value for estimation of GFR (eGFR) was derived from five different formulas either over-estimated or underestimated GFR as referenced to rGFR, and the extent of deviations was dependent on gender, age and CKD stage. The Counahan-Barratt formula and the Schwartz formula gave the most accurate estimations of GFR for CKD stages 1 and 2-3, respectively regardless of gender and age differences. Receiver operating characteristic analyses indicated that the Counahan-Barratt formula has the highest diagnostic accuracy.The Counahan-Barratt formula provides the best approximation to rGFR, thereby the highest applicability to Chinese children with CKD of different genders, ages and CKD stages.