We applied a variety of methods to follow the course of kainic acid (KA) induced retinal apoptosis, especially with regard to the spatial and temporal aspects. At 24 h after KA injection, a massive cell increase, which showed terminal transferase-mediated dUTP nick-end-labeling technique positive signals, was observed in all of the retinal layers, with the exception of the outer nuclear and photoreceptor layers. Electron microscopy further confirmed that these cells might be apoptotic body ingesting phagocytes, whose function seemed to correlate with bcl-2 mRNA up-regulation. When histochemical studies were performed to determine the cellular identity of the phagocytes, the microglia were thought to be the one and only type of phagocytes involved in the KA-induced retinal apoptosis. In conclusion, we demonstrated that after KA injection, microglia were the only phagocytes to participate in clearing apoptotic debris from the inner retinal layers, and that their function might correlate with the change in expression of the bcl-2 gene family.