Estimates of glomerular filtration rate (eGFR) have become popular in clinical medicine as an alternative to measuring GFR (mGFR) but there are few studies comparing them in clinical practice. We determined mGFR by iohexol clearance in 81 consecutive children in routine practice and calculated eGFR from 14 standard equations using serum creatinine, cystatin C, and urea nitrogen that were collected at the time of the mGFR procedure. Non-parametric Wilcoxon test, Spearman Correlation, Bland–Altman analysis, bias (median difference) and accuracy (P15, P30) were used to compare mGFR to eGFR. For the entire study group, the mGFR was 77.9±38.8mL/min/1.73 m2. Eight of the 14 estimating equations demonstrated values without a significant difference from the mGFR value and demonstrated a lower bias in Bland–Altman analysis. Three of these eight equations based on a combination of creatinine and cystatin C, (Schwartz et al. 2009, 2012; Chehade et al.), had the highest accuracy with approximately 60% of P15 and 80% of P30. In 10 patients with a single kidney, seven with kidney transplant, and 11 additional children with short stature, values of the three equations had low bias and no significant difference when compared with mGFR. In conclusion, the three equations that employed cystatin C, creatinine, and growth parameters performed in a superior manner over univariate equations based on either creatinine or cystatin C, and also had good applicability in specific pediatric patients with single kidneys, those with a kidney transplant, and/or short stature. Thus, we suggest that eGFR calculations in pediatric clinical practice employ only a multivariate equation.