AIMS: Current estimated glomerular filtration rate (eGFR) equations may be inaccurate in patients with spina bifida (SB) because of reduced muscle mass and stature. Cross-sectional and longitudinal variability of eGFR were analyzed in these patients across multiple equations, hypothesizing greater variability in creatinine-based than cystatin-C (Cys-C)-based equations. METHODS: This retrospective cohort study included children (age, 1-17.9 years) and adults (≥18 years) with SB from 2002-2017 at a large SB clinic. Those without all data needed to calculate eGFR were excluded. Four pediatric and three adult eGFR equations were compared for cross-sectional outcomes of eGFR and elevated office blood pressures using chronic kidney disease (CKD) stage classification, and for longitudinal outcome of eGFR slope over time using covariance pattern models accounting for repeated measures. RESULTS: One hundred and eighty two children and 75 adults had greater than or equal to 1 set of data measurements; 118 and 52, respectively, had greater than or equal to 2 sets. The pediatric bedside Schwartz equation had the highest median eGFR and coefficient of variation. CKD stage classification by eGFR showed large differences across equations in children, with rates of eGFR < 60 and <90 ml/min/1.73 m(2) ranging from 2%-9% and 5%-69%, respectively. Only one equation showed a significant inverse association between eGFR and blood pressure. Longitudinally, eGFR slopes over time were different across pediatric equations (P < .001) but not adult equations. The bedside Schwartz equation had a positive eGFR slope; the other Cys-C-containing equations had negative slopes. CONCLUSIONS: Creatinine-based equations in children with SB vary considerably from cystatin-C-containing equations in calculating both single point-in-time eGFR values and eGFR trends over time.