PURPOSE: To study whether apolipoprotein E (APOE) genotypes are associated with risk for developing cataract and age-related macular degeneration (AMD). METHODS: A sample of 88 healthy adults (50-75 years) genotyped for polymorphisms of APOE underwent an eye examination which included visual acuity (VA) testing, slit-lamp cataract evaluation, optical coherence tomography (OCT) and fundus photography, the last of which was analysed and graded for macular pathology at the Reading Centre, Moorfields Eye Hospital, London. Two-by-two cross tables were analysed using the Fisher-Boschloo unconditional full multinomial test. Two-sample t-tests were used for comparing means of scale variables. RESULTS: Thirty-two participants were diagnosed with cataract or had undergone cataract surgery in one or both eyes, and 56 participants demonstrated no signs of cataract. We found that APOE4 carriers were less likely to have cataract than non-APOE4 carriers (p = 0.039). No correlation between APOE genotypes and morphologic changes in the macular region was revealed. However, APOE3 carriers disclosed significantly higher average macular thickness in both eyes than non-APOE3 carriers (p = 0.012), and APOE3 carriers also had significantly better VA than non-APOE3 carriers (p = 0.041). CONCLUSIONS: We found no association between AMD and APOE polymorphism in a population of 96 individuals aged 50-75 years. A weak negative association between APOE4 and cataract was uncovered in the same population. Apolipoprotein E3 may be a protective factor against the loss of nerve fibres in the macular region.