Estimation of glomerular filtration rate (GFR) from serum creatinine (Scr) or cystatin C (Cys C) exhibit variable performances. We compared the performances of 14 Scr and 9 Cys C estimated GFR equations using inulin clearance (Clin) as the reference test in 103 stable renal transplant populations. Bias, precision, receiving operation characteristics (ROC), accuracy within 30% ranges from the reference method and agreements of each test were compared. Mean Clin was 46.4+/-20.9 ml/min/1.73 m2. Scr and Cys C levels correlated well with each other (r=0.83, P<0.0001) and with Clin (r=-0.57 and -0.53, P<0.001, respectively). ROC analysis demonstrated no superiority of Cys C over Scr. Gats equation achieved the highest accuracy of 70% in patients with GFR>or=60 ml/min/1.73 m2. In patients with GFR>or=60 ml/min/1.73 m2, the Nankivell equation demonstrated the highest accuracy of 73.91%. Cys C-based equations were not depicted to be thoroughly accurate. Bias, precision and agreement were otherwise similar in all GFR tests. Scr-based equations did not appear to be inferior to Cys C-based equations as a means to estimate GFR in renal transplant patients.