OBJECTIVE To determine the structural changes in the retinal pigment epithelium (RPE) and neighboring structures induced by intravitreal injection of a lysosomal protease inhibitor. METHODS Eleven-week-old Sprague-Dawley rats were injected with 5 microliter of a lysosomal protease inhibitor, E-64 (2.22 microM), intravitreally once and killed at 24 hours, 48 hours, or 7 days later. Others received two or three injections at 48-hour intervals or three daily injections, and killed at 1, 4, and 7 days after the last injection. Eyes were enucleated and retinal tissues were processed for light and electron microscopy. RESULTS A single injection of E-64 caused only a transient accumulation of phagosome-like and phagolysosome-like inclusion bodies in the RPE. By contrast, repeated injection caused progressive accumulation of these inclusions followed by altered RPE cell conformation, and changes in organelles such as loss of smooth endoplasmic reticulum (SER). This was accompanied by shortening and loss of photoreceptor outer segments without prior dysmorphic changes, alteration of choroidal capillaries, and invasion of Bruch's membrane by fibroblasts and pericytes. Intravitreal injection of vehicle as control induced no structural changes. CONCLUSIONS E-64 treatment induced structural changes in the outer retina. The causal relationship between accumulation of inclusions in RPE and changes in other subcellular organelles and neighboring cells systems is not clear. However, there are possible explanations: physical disturbance of organelles, particularly SER by inclusions; cellular damage by consequent upon accumulation of A2-E; or, shortage of recycled material due to reduced degradation of phagosomes.