Objective: Our aim was to determine whether cystatin C level has a superiority to creatinine to assess kidney functions in rapid decreases of glomerular filtration rate due to acute mercury exposure in children. Eight different glomerular filtration rate calculation formulas which have been used creatinine and/or cystatin C were also compared. Methods: Serum urea, creatinine and cystatin C values of 39 mercury exposed children were measured. Glomerular filtration rates were calculated by eight different formulas. Patient group was divided into three subgroups according to mercury levels. Results: Cystatin C and mercury levels of the patients were found significantly different from control group (p<0.001). There was not a significant difference in creatinine and urea values between two groups (p=0.913, p=0.236). There was not a significant difference between patient and control groups in GFR calculations which have been used serum creatinine and height or which have been used urea additional to them (p=0.069, p=0.559, p=0.424, p=0.945, respectively), but there was a significant difference between patient and control groups in GFR calculations which have been used cystatin C only or creatinine, urea and height in addition to this (p<0.001, p<0.001, p=0.042, p<0.001, respectively). In sugroup analysis, cystatin C results and the results of three GFR calculations of four GFR calculations which were used cystatin C were found different in control group according to subgroups but there was not a difference between subgroups. Conclusion: Cystatin C level is a better indicator than creatinine to assess kidney functions in rapid decreases of glomerular filtration rate due to acute exposure of mercury. Formulas using cystatin C gave better results than formulas using creatinine and height in estimation of glomerular filtration rate.