Glomerular filtration rate (GFR) estimated by creatinine- and/or cystatin C-based equations (eGFR) is widely used in daily practice. The purpose of our study was to compare new and old eGFR equations with measured GFR (mGFR) by iohexol clearance in a cohort of children with chronic kidney disease (CKD). We examined 96 children (median age 9.2years (range 0.25-17.5)) with CKD stages 1-5. A 7-point iohexol clearance (GFR7p) was defined as the reference method (median mGFR 66mL/min/1.73m2, range 6-153). Ten different eGFR equations, with or without body height, were evaluated: Schwartzbedside, SchwartzCKiD, SchwartzcysC, CAPA, LMREV, (LMREV + CAPA) / 2, FAScrea, FAScysC, FAScombi, FASheight. The accuracy was evaluated with percentage within 10 and 30% of GFR7p (P10 and P30). In the group with mGFR below 60mL/min/1.73m2, the SchwartzcysC equation had the lowest median bias (interquartile range; IQR) 3.27 (4.80) mL/min/1.73m2 and the highest accuracy with P10 of 44% and P30 of 85%. In the group with mGFR above 60mL/min/1.73m2, the SchwartzCKiD presented with the lowest bias 3.41 (13.1) mL/min/1.73m2 and P10 of 62% and P30 of 98%. Overall, the SchwartzcysC had the lowest bias - 1.49 (13.5) mL/min/1.73m2 and both SchwartzcysC and SchwartzCKiD showed P30 of 90%. P10 was 44 and 48%, respectively. The SchwartzcysC and the combined SchwartzCKiD present with lower bias and higher accuracy as compared to the other equations. The SchwartzcysC equation is a good height-independent alternative to the SchwartzCKiD equation in children and can be reported directly by the laboratory information system. ClinicalTrials.gov , Identifier NCT01092260, https://clinicaltrials.gov/ct2/show/NCT01092260?term=tondel&rank=2.