In human skin, the 3895-bp deletion of mitochondrial DNA (mtDNA(3895)) is catalysed by ultraviolet (UV) light through the generation of reactive oxygen species. Given its function in vision, the human eye is exposed to oxidising UV and blue light in its anterior (cornea, iris) and posterior (retina) structures. In this study, we employed a highly sensitive quantitative PCR technique to determine mtDNA(3895) occurrence in human eye. Our analysis shows that the mtDNA(3895) is concentrated in both the cornea and the retina. Within the cornea, the highest mtDNA(3895) level is found in the stroma, the cellular layer conferring transparency and rigidity to the human cornea. Moreover, mtDNA(3895) accumulates with age in the stroma, suggesting a role of this deletion in corneal ageing. Within the retina, mtDNA(3895) is concentrated in the macular region of both the neural retina and the retinal pigment epithelium, supporting the hypothesis that this deletion is implicated in retinal pathologies such as age-related macular degenerescence. Taken together, our results imply that UV and blue light catalyse mtDNA(3895) induction in the human eye.