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Purpose Cystatin C has proposed as a surrogate of serum creatinine (Scr). The elderly population accounts for the largest proportion of the chronic kidney disease (CKD) patients. The aim of this study was to assess the diagnostic value of serum cystatin C and compare the applicability of cystatin C-based equations with Scr-based equations for estimating glomerular nitration rate (GFR) in Chinese elderly population. Methods The estimated GFR (eGFR) values from three cystatin C-based equations (Maclsaac, Tan and Ma) and three Scr-based equations (CG, MDRD, CKD-EPI) were compared with the reference GFR (rGFR) from 99mTc-DTPA renal dynamic imaging method. Results 110 elderly Chinese (60-92 yr, 71.05 ± 7.62 yr) were enrolled. Cystatin C had better diagnostic value than Scr (relationship coefficient with rGFR: cystatin C -0.847 vs. Scr -0.729, P < 0.01; sensitivity: cystatin C 0.90 vs. Scr 0.55, P < 0.01; AUCROC: cystatin C 0.857 vs. Scr 0.757, P < 0.01). The precision of each equation was acceptable, except the MDRD equation. Cystatin C-based equations predicted more accurate than Scr-based equations. In rGFR < 60ml/min/1.73m2 levels, the superiorities of cystatin C-based equations were embodied more remarkable. Of the selected six equations, the Maclsaac equation achieved the largest accuracy and the least bias. Conclusions Cystatin C could be a promising kidney function marker. Cystatin C-based equations may be more suitable than Scr-based equations for Chinese elderly population. Presently, the Maclsaac equation could be the optimal.