Kidney transplantation is the preferred modality of treatment in children with end stage kidney disease. Azathioprine (AZA) is from the oldest group of immunosuppressive therapy but in recent transplant era it has been mostly replaced by Mycophenolate mofetil (MMF). In this longitudinal study the result of kidney transplantation in children on AZA and MMF is compared. Medical records of all children who had been transplanted in Shiraz from the beginning of transplantation program and who had pediatric nephrologist follow up, were gathered either during their last referral and when expired or returned to dialysis from their medical files. Mean serum creatinine of children who had been on MMF was compared with those who had been on cellcept. Their immunosuppressive regimens were otherwise similar. SPSS15.1 software and T-Test and Pearson correlation test were used for Statistical analysis. From the 216 children ≤ 19 years old at Tx between 1992 and 2007, 138 children was followed by pediatric nephrologist. There were 79(57.2%) boys and age at Tx was 3-19 years with a Mean+/-SD of (13.6+/-3.5) and minimum weight of 10 kg. Donor ages were 1to52 years with a mean of (24.6+/-12.5) with 41 parents, 9 siblings and other relatives, 67 deceased and 21unrelated. Their Primary renal diseases consisted of glomerular diseases, hereditary diseases, reflux-obstruction dysplasia, stone and unknown in 26(19%), 47(34%), 58(42%), 2(1.5%) and 5(3.5%) respectively. The mode of dialysis before transplantation was hemodialysis in the majority of our cases (85.5%), followed by preemptive transplantation (12.1%). Their immunosuppressive regimen included prednisolone, cyclosporine A and either AZA or MMF. Thirty seven allocated to AZA and 92 to MMF group. Nine children took neither azathioprine nor cellcept 7 due to primary non-functioning of graft. Regarding the result of Tx in MMF group or AZA group, after exclusion of 7 children with primary non-functioning of graft and 2 who didn’t take AZA or cellcept, 11 out of 92(12%) children in MMF group either expired or returned to dialysis but in AZA group 8 out of 37(21.5%) did so, 2 children in the later group died with normal renal function. Children in the AZA and MMF group had a follow up of 98.08 ± 38.72 and 60.64 ± 38.42 months respectively. The Mean of last serum creatinine was 2.36 ± 2.5 and 1.64 ± 1.66mg/dl respectively. From the children in AZA group 6 returned to dialysis after a mean period of 77.6 months and from the MMF group 6 returned to dialysis after a mean time of 20.16 months. In conclusion, by considering the longer follow up in AZA group the result of transplantation is more or less similar with AZA and MMF.