The present study evaluated the effects of proton and gamma-ray ionizing radiation on the mouse eye. The aim of this work was to analyze radiation-mediated retinoid oxidation in the retina and retinal pigment epithelium (RPE). The findings from this analysis can be used to develop a noninvasive method for rapid assessment of the effects of ionizing radiation. Comparative fluorescence and chromatographic analyses of retinoids before and after irradiations were performed. The fluorescent properties of chloroform extracts from irradiated mouse retina and RPE exhibited an increase in fluorescence intensity in the short-wave region of the spectrum (λ < 550 nm). This change is due to increased retinal and RPE retinoid oxidation and degradation products after radiation exposure. Comparative analyses of radiation effects demonstrated that the effect of proton exposure on the retina and RPE was higher than that of gamma-ray exposure. The present study revealed a new approach to assessing the level of radiation exposure in ocular tissues.