AIM: To derive an accurate prediction model for estimating glomerular filtration rate (GFR) in children based primarily on the endogenous renal function marker cystatin C (CysC) and body cell mass (BCM). THEORY: Cystatin C is produced at a constant rate in all cells of the body and is excreted by glomerular filtration followed by catabolization in the tubular cells. We hypothesized that production rate is proportional to body cell mass (BCM) and inferred GFR (mL/min) to be proportional to BCM/CysC. MATERIAL AND METHODS: GFR was determined with 51Cr-EDTA-clearance in 131 children (52 girls, 79 boys) aged 2-14 years. GFR was 14-147 mL/min/1.73m2. BCM was estimated using bioimpedance spectroscopy. Log-transformed data on BCM/CysC, serum creatinine (SCr), body-surface-area (BSA), height×BSA/SCr, CysC, weight, sex, age, height, serum urea and albumin were considered possible explanatory variables using robust regression in a forward, stepwise procedure. GFR (mL/min) was the dependent variable. The accuracy and precision of the prediction model were compared to other prediction models from the literature, using k-fold cross-validation. Local constants and coefficients were calculated for all models. RESULTS: New prediction equation GFR (mL/min) = (BCM/CysC)^0.39×(heightxBSA/SCr)^0.65×10.2 could predict 99% within ±30% of reference GFR, and 66% within ±10%. This was higher than all other equations. The present equation also had the highest R2 and the narrowest 95% limits of agreement. CONCLUSION: The new equation predicts GFR with higher accuracy than other equations. Endogenous methods are, however, still not accurate enough to replace exogenous markers when GFR must be determined with high accuracy.