The introduction of cyclosporine (CsA) has improved the clinical results of renal transplantation significantly; however, these improvements were closely associated with an increased incidence of renal dysfunction. The present study sought to examine the ultrastructural changes in renal allografts with CsA nephrotoxicity. Nine patients who underwent renal transplantation at the Baskent University Faculty of Medicine between 2001 and 2002 were examined; 26 biopsies of these nine patients who had received their first renal allograft were included in this study. All patients with CsA toxicity showed some form of glomerular endothelial cell injury. The swelling of mitochondria was present in three of nine renal allografts with CsA toxicity, and podocyte changes were found significantly more frequently among patients with CsA toxicity. In addition, focal segmental thickening and the duplication of glomerular basement membrane were observed statistically more frequently. In conclusion, these findings could help differentiate CsA toxicity from other conditions and develop better treatment strategies.