Cystatin C (CysC) may be a better marker of glomerular filtration rate (GFR) than serum creatinine (SCr) level. Few studies derived CysC-based GFR prediction equations for children. Objectives of this study are to: (1) derive CysC-based GFR prediction equations for children, and (2) compare these equations with published formulae. Patients younger than 18 years undergoing iothalamate GFR (IoGFR) testing were studied prospectively. Data collected were age, sex, CysC level, SCr level, IoGFR, height, weight, and diagnosis. By using linear regression, 2 equations were derived and compared with 3 previously published formulae by using Bland-Altman analysis and diagnostic characteristics. Local coefficients were derived for comparison formulae. There were 111 GFR tests from 103 patients (age, 12.7 +/- 4.7 years; IoGFR, 73.6 +/- 35.7 mL/min/1.73 m(2) [1.23 +/- 0.60 mL/s/1.73 m(2)]; 60% male; and 25% post-renal transplantation). The 2 equations derived were the CysEq (including CysC level) and the CysCrEq (including CysC and SCr levels). Overall, the 2 new equations had bias and precision similar to previously published formulae when local coefficients were used. However, in patients with a renal transplant or spina bifida, the 2 new equations were less biased and more precise. All CysC-based equations performed better than the Schwartz formula. This study provides 2 CysC-based GFR prediction equations that are accurate, precise, and sensitive for detecting abnormal GFRs. Three previously published CysC GFR prediction equations have been validated for the first time. Prediction equations based on CysC level are likely to provide more accurate estimates of GFR than SCr-based equations.