Abstract Background: The development of continuous curvilinear capsulorrhexis (CCC) has contributed significantly to the tolerability and effectiveness of cataract extraction and intraocular lens implantation. Staining of the anterior capsule has become a popular method of increasing visibility when performing CCC. Objective: The aim of this study was to determine, using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), the highest concentrations of trypan blue dye that would not cause long-term toxicity after injection into the anterior chamber of rat eyes. Methods: The eyes of healthy female albino Wistar rats were used in this investigator-masked, controlled, 2-period, experimental study conducted over 12 weeks at the Dicle University Experimental Animal Laboratory, Diyarbakir, Turkey. The rats were randomly divided into 5 groups of 4 using a random-number table. Each rat was administered a 0.05-mL injection of trypan blue into the right eye in 1 of the following concentrations: 0.4%, 0.2%, 0.1%, 0.05%, or 0.025%. A 0.05-mL pH-balanced saline solution was injected into the left eye of each rat to act as a control. At 1 day after injection and 4 weeks after injection (early period), 1 rat from each concentration group was euthanized and their eyes were enucleated. At 12 weeks after injection (late period) the remaining 2 rats from each group were euthanized and their eyes were enucleated. Corneal endothelial cells and the anterior lens capsule of the enucleated eyes were analyzed using SEM and TEM, and the results were compared with those of the control group. In the TEM analysis, the primary end point was the histopathologic changes in the cellular organelles when compared with those in the control group. In the SEM analysis, the primary end point was changes in cell shape, intracellular junctions, and density of the microvilli when compared with those in the control group. Results: Forty eyes from 20 albino Wistar rats (mean [SD] age, 8.2 [1.6] weeks; mean [SD] weight, 175.6 [16.5] g) were used in the study. Each group of rats received a different concentration of trypan blue in the right eye. In the early period, both the 0.4% and 0.2% concentrations were associated with the impairment of the hexagonal structure of corneal endothelial cells and intercellular junctions. Those concentrations were also associated with an increased occurrence of cellular vacuolation, cytoplasmic edema, extensive granulation of the endoplasmic reticulum, pyknotic nuclei, and mitochondrial degeneration. In the late period, these changes were observed as persisting in a decreasing manner. With the 0.1% and 0.05% concentrations, the density of microvilli decreased, nuclei appeared normal, granulation of the endoplasmic reticulum and Golgi apparatus was active, and minimal levels of mitochondrial degeneration were observed. Conclusions: In this small experimental study in rat eyes, trypan blue at concentrations >0.025% was associated with impaired morphology and structure of corneal endothelial cells after short-term exposure. This effect continued in a decreasing fashion after long-term exposure. No significant changes were noted in the control group or the group administered the 0.025% concentration.