There is a global effort to standardize clinical laboratory serum creatinine measurements to the reference method of isotope-dilution mass spectrometry (IDMS). Creatinine values in serum and urine are frequently used in children to calculate creatinine clearance (mCrCl) or estimate glomerular filtration rate (GFR) by Schwartz's equation (eGFR). The original normative data of mCrCl and eGFR were developed using Jaffe method. To investigate what impact the differences in methodologies of creatinine analysis will have on mCrCl and eGFR, we measured creatinine in random serum and urine samples by three commercially available assays: Jaffe (J), enzymatic (E) and enzymatic method traceable to IDMS (E-IDMS). There was a significant bias in the two enzymatic methods when compared with J method. The theoretical predicted errors in overestimating mCrCl ranged from 1.10 to 1.34 by E and 1.20 to 1.54 by E-IDMS; and in calculating eGFR 1.07-1.16 by E and 1.30-1.46 by E-IDMS, which was further confirmed in children who had formal GFR evaluation. Thus, as the clinical laboratories calibrate their creatinine assays to the gold standard IDMS method, it is important for the pediatric nephrology community to develop new equations for estimation of GFR based on the new creatinine assay.