Abstract: 11 otter rabbits that spontaneously infected with Encephalitozoon cuniculi and 5 healthy white rabbits with long ears were used in this experiment for studying the apoptosis of renal cells. The results showed that apoptotic cells mainly occurred in the renal cells of distal convoluted tubule and collecting duct. Under transmission electron microscope, in the early stage of cell apoptosis, chromatins were highly condensed and became marginal, rough endoplasmic reticulum increased in number and expanded in shape till showing vacuolated; in the final stage, cytoplasm became shrank, membranes occurred blebs, nuclei were coagulation of mass, finally apoptotic bodies which were surrounded by wrinkled membranes formed. The TUNEL staining of renal tissues showed that nuclei were concentrated and nuclear membranes became thicken and shrank in the early stage; finally apoptotic bodies with wrinkled membranes formed. The results of flow cytometer tests were as follows: sub “G1” apparently appeared in the sick rabbits, there was statistical significance about the numbers of apoptotic cells between sick rabbits and control rabbits (P=0.01) and the renal cell cycles of sick rabbits also changed. The above results manifested that the numbers of apoptotic cells in sick rabbits were higher than that of control rabbits.