Serum cystatin C has been shown to be a more sensitive marker for measurement of GFR, but it is not available for clinical use in all laboratories. Since the accurate estimate of GFR is important for clinical decision making in renal transplant recipients, we planned a study to compare several cystatin C-based equations with creatinine-based estimates to find the best practical model for GFR calculation in adult renal transplant recipients. The study group was consisted of 70 renal transplant recipients from living donors (46 males and 24 females) with stable kidney function. Patient’s data including age, gender, weight, BMI, kidney source and immunosuppressive drugs were collected on recipient’s visit. Then blood samples were collected for measurement of serum creatinine, cystatin C and serum albumin. Patients GFR calculated by Cockcroft-gault, modification of diet in renal disease (MDRD), abbreviated MDRD and five cystatin C-based equations .Then data analyzed by SPSS program. The mean age of recipients was 38.7 ± 13.4 years. All of patients were on cyclosporine, mycophenolate mefotil and prednisolone. The mean GFRs were (67.1 ± 25.9 ml/min/1.73 m2) by Cockgraft-gault, (61 ± 17.7 ml/min/1.73 m2) by abbreviated MDRD,(60 ± 18.6 ml/min/1.73 m2)by MDRD formula. Cystatin-C based GFR calculated with five different equations were (43.6 ± 16.2), (44 ± 13.2), (33.8 ± 14.1), (35.6 ± 13.7) and (36.9 ± 13.6) ml/min/1.73 m2 by Filler, Lebricon, Larsson, Rule and Hoek equations respectively. There was a significant difference between cystatin C-based equations in comparison to creatinine-based estimates (P< 0.001). However we found a statistical difference between creatinine-based estimates and cystation C-based equations GFR, the MDRD formula results is closer to cystatin C GFR in our study. We recommend that until introduction of a more accurate model for practical application, MDRD equation is a better substitute for GFR calculation in our renal Tx recipients.