Purpose To investigate the influence of ionizing radiation on the corneal epithelium and endothelium of rabbit eyes. Methods Five healthy mature albino rabbits were unilaterally irradiated with 20 Gy of X-rays (250 kV, 12 mA). Slit-lamp biomicroscopic observation and specular microscopic examination of the corneal epithelium and endothelium were carried out before and 1, 4,8,12,16,20,24, and 36 weeks after irradiation. We evaluated mean area of the superficial corneal epithelial cells, mean area and the percentage of hexagonal cells of the corneal endothelial cells, and corneal thickness. The statistical difference between the irradiated and control eyes was assessed using paired t-test. Results All animals developed cataract within 24 weeks. Slit-lamp biomicroscopy showed no apparent corneal abnormalities over the 36-week follow-up period. Specular microscopy revealed a significant enlargement of the superficial corneal epithelial cells from 4 to 12 weeks after irradiation (Po0.01), which disappeared at 16 weeks post-irradiation. Specular microscopy of the corneal endothelium showed enlargement and morphological alterations of the cells beginning 8 weeks after irradiation (Po0.05). These changes persisted throughout the study period. There were no statistically significant changes in corneal thickness. Conclusion After X-ray radiation of 20 Gy, transient damage occurred in the corneal epithelium, while delayed and irreversible changes were seen in the endothelium.