Acute rejection is the most important threat to transplanted kidneys in the early phase after transplantation. With the advances in renal transplant surgery and immunosuppressive therapies, one-year graft survival rates reached 90%, but long-term graft survival did not improve to a similar degree. To prevent acute rejection more effectively and decrease the risk of chronic nephropathy development, the pathogenesis and effects of acute rejection on renal grafts should be further explored. This study aimed to examine the glomerular and tubular changes ultrastructurally. Tissues were obtained from 11 renal allografts with acute rejection, fixed in 1% Osmium tetra oxide embedded in Epon. The changes in glomerular basement membrane, podocyte, mesangium, and proximal tubules were examined by electron microscope. Tubular changes such as tubular basement membrane multi-lamellation, MN and PMN cells in peritubular capillaries, tubular vacuolization, mitochondrial changes (increase in number, alterations in cristae organization, or cristae effacement), and infiltration of tubular epithelium by MN cells (mainly lymphocytes) were found statistically significant (p < 0.01) when compared to those of control group. Some forms of endothelial injury (swelling of endothelial cells or fenestrae loss) were also statistically significant (p < 0.01). Acute rejection is an important predictor of long-term graft survival, and there may be no clinical clue to make diagnosis easier. Therefore ultrastructural changes may help solve this problem together with molecular studies.