Background and objectives The diagnostic accuracy of cystatin C estimated GFR (eGFR) by various cystatin C equations have varied in different studies. We hypothesized that the GFR level of enrolled patients affects the diagnostic accuracy of a cystatin C equation. Design, setting, participants, & measurements We analyzed 240 consecutively enrolled children at a single Canadian center in a prospective and cross-sectional study. Cystatin C was analyzed with nephelometry, and cystatin C eGFR was estimated by the equations validated in children. GFR was measured by technetium- 99m-diethylene-triamine penta-acetic acid (99mTc DTPA). Results We compared various cystatin C equations across GFR strata <60, <90, ≥135, and ≥150 ml/min per 1.73 m2 for an accurate prediction and appropriate classification of the measured GFR. The CKiD, Zappitelli- CysEq, and Zappitelli-CysCrEq equations had a higher accuracy, estimated by eGFR values within 10% and 30% of the respective 99mTc DTPA, in the GFR categories <60 and <90 ml/min per 1.73 m2, whereas the Bökenkamp, Bouvet, and Filler equations had a greater accuracy in the GFR categories ≥135 and ≥150 ml/min per 1.73 m2. The Bouvet, CKiD, Filler, Zappitelli-CysEq, and Zappitelli-CysCrEq equations had a greater sensitivity to classify GFR <60 and <90 ml/min per 1.73 m2, whereas the Bökenkamp equation had a higher sensitivity for GFR ≥135 and ≥150 ml/min per 1.73 m2. Conclusions The diagnostic accuracy of various cystatin C equations varies with GFR. This issue needs consideration while applying these equations in clinical practice and for further research on eGFR equations. © 2011 by the American Society of Nephrology.