Studies in the central nervous system (CNS) and retina have revealed the significance of docosahexaenoic acid (DHA), an essential omega-3, 22 carbon 6 double bond (22:6), fatty acid. DHA is necessary for various functions in the CNS, including neuronal membrane bio- and synaptogenesis in memory and vision, and it is the precursor for docosanoids and neuroprotectin D1 (NPD1; 10R,17S-dihydroxy-docosa-4Z,7Z,11E,13E,15Z,19Z hexaenoic acid), a DHA bio-derivative with neuroprotective properties. This review covers three targets in ophthalmology for mediator lipidomics, a subgroup within the field of metabolomics: inflammation, neuroprotection and nerve regeneration. It also discusses the role DHA, NPD1 and other lipid mediators play in these three areas.