Background: Accurate and rapid assessment of allograft function is essential in renal transplant recipients in order to detect allograft rejection and to monitor drug nephrotoxicity. We aimed to evaluate the usefulness of cystatin C as a marker of kidney allograft function in the early post-transplant period and to compare this value with that of conventional serum creatinine concentration. Methods: Twenty four patients scheduled for kidney transplantation at the Kidney Transplant Center of Ghaem Hospital, Mashhad, Iran from September 2006 to November 2007, were sequentially enrolled into the present study. Serum creatinine and cystatin C concentrations and urine output were measured daily after transplantation for 3 weeks or until discharge from the hospital. Results: On the 3rd postoperative day, with a cut-off value of 75 mL/min for glomerular filtration rate, areas under the receiver operating characteristic (ROC) curves were 0.926 for creatinine (P=0.021) and 0.815 for cystatin C (P=0.088). At this point creatinine was more sensitive and specific than cystatin C in estimating glomerular filtration rate. On the 7th day after transplantation, areas under ROC curves were 0. 893 for creatinine (P=0.066) and 1.000 for cystatin C (P=0.017). Therefore, cystatin C was more sensitive and specific than creatinine in estimating glomerular filtration rate. In two patients with acute rejection and arterial thrombosis, serum cystatin C concentrations increased earlier than serum creatinine. Conclusion: There is a correlation between creatinine and cystatin C early after kidney transplantation. Serum creatinine levels seem to be more sensitive and specific for detecting transitory changes in renal function in the 1st week after transplantation. After the 1st week after transplantation, cystatin C was more sensitive and specific than serum creatinine concentration.