Background: The measurement of glomerular filtration rate (GFR) applying serum creatinine (Cr) does not reflect the GFR of patients accurately, and thus recently, studies on the measurement of GFR applying serum cystatin-C (Cys-C) have been conducted. We investigated the relationship between Cys-C and proteinuria in patients with chronic kidney disease. Methods: We compared the biochemical test, including serum Cys-C, the amount of proteinuria and the concentration of Cys-C measured by the 24-h urine test, and the difference of GFR on 105 patients who visited our hospital in 6 months (January to June 2007). Results: Among 105 patients, 58 patients were males, and the mean age was 56.74 ± 16.31 years. With regard to underlying diseases, the group with diabetes had 76 patients and the group showing nephrotic proteinuria [nephrotic syndrome (NS)] had 29 patients. The GFR-Cys-C in the NS group (44.17 ± 26.32 mL/min) was higher than in the non-NS group (33.68 ± 14.29 mL/min; p = 0.041). The fractional excretion (FE) of Cys-C increased according to FE of albumin ( p = 0.000) and GFR-modification of diet in renal disease (MDRD) equation (p = 0.000). Serum Cys-C increased according to corrected urine Cys-C (p = 0.010). The GFR calculated by serum Cys-C decreased according to FE of albumin (p = 0.003). The degree of difference between GFR-Cys-C and GFR-MDRD was negatively correlated according to the FE of albumin (p = 0.001). Conclusion: We confirmed that urinary excretion of Cys-C could be altered by previously known mechanisms such as proteinuria. Difference between GFR-Cys-C and GFR-MDRD was negatively correlated according to FE of albumin.