Apoptosis is a form of cell death distinct from necrosis showing distinctive morphologic features and may require energy. It is under various control mechanisms and may involve an endonuclease, which cleavages genomic DNA in the internucleosomal linker regions. Previously, we reported that ischemic/reperfusion injury to rat retina induced endonuclease mediated apoptosis of retinal neurons. In this study, we examined the effect of aurintricarboxylic acid (ATA), an endonuclease inhibitor, on ischemia/reperfusion damage in rat retina in our established rat model. A single intraperitoneal injection of ATA at 2 mg/kg given immediately after 60 minutes of ischemia to the retina showed no observable effect. At 10 mg/kg, there was notable beneficial effect morphologically but not morphometrically. ATA at 100 mg/kg showed significant effect both morphologically and morphometrically. This observation is consistent with the hypothesis that endonuclease mediated apoptosis may be involved in retinal cell loss after ischemia/reperfusion insult.