We report on the relationships between serum cystatin C level, glomerular filtration rate (GFR) estimated from a cystatin C-based prediction equation (that of Filler and Lepage), GFR calculated by the Schwartz formula and technetium 99m-diethylene triamine penta-acetic acid ((99)Tc-DTPA)-determined GFR in 28 children with spina bifida. All children underwent measurement of height, weight, serum cystatin C level, and serum creatinine level at the time of their renal scan. The relationship between variables was assessed by Pearson correlation. Pearson correlation for the relationship between (99)Tc-DTPA GFR and GFR calculated by the cystatin C-based equation was significant and higher than that of the relationship between (99)Tc-DTPA GFR and GFR calculated by the Schwartz equation, which was not statistically significant. The correlation for Filler GFR was 0.42 (P = 0.03) and for Schwartz GFR was 0.21 (P = 0.28). Although we use renal scan determination of GFR as the best measure, and a creatinine-based formula as the most practical measure, perhaps a formula such as that published by Filler and Lepage, which is not dependent on anthropometric data, might be a more useful (and accurate) tool for establishing GFR in children with spina bifida.