The purpose of this article is to review the literature on relationships between the intestinal microbiota and ocular inflammatory disease, specifically non‐infectious uveitis and age‐related macular degeneration. The importance of the intestinal microbiota in uveitis pathogenesis has been shown by multiple groups demonstrating that alterations in the microbiota induced by certain oral antibiotics results in reduced uveitis severity, and another group demonstrating that a commensal intestinal bacterial antigen activates retina‐specific autoreactive T cells, potentially indicating a commensal trigger for uveitis. Additionally, commensal intestinal bacterial metabolite short chain fatty acids can be utilized to suppress autoimmune uveitis. Age‐related macular degeneration is associated with intestinal dysbiosis, which is partially influenced by genetic risk alleles and AREDS supplementation. Strategies for therapeutically targeting the intestinal microbiota might involve several approaches, including the use of antibiotics, dietary changes, drugs that supplement beneficial bacterial metabolites or target causative bacterial strains, dietary strategies or faecal microbial transplantation. In summary, the intestinal microbiota are at the cross‐roads of genetic and environmental factors that can promote ocular conditions such as non‐infectious uveitis and age‐related macular degeneration, partially via its dynamic influence on mucosal and systemic immunity. The intestinal microbiome thus represents a salient potential target for therapeutic modulation to treat these potentially blinding conditions.