Mitochondrial dysfunction is integral to the pathophysiology of a number of ocular disease states, including diabetic retinopathy, age-related macular degeneration, and glaucomaGlaucoma. In recent years, a novel non-invasive imagingImaging modality has been developed that may detect pre-structural metabolic dysfunction that occurs in the retinaRetina in each of these disease states. This technology specifically quantifies mitochondrial stress and has been used to study both the maculaMacula and the optic nerveOptic nerve head. Most exciting is its use in monitoring treatment response in diabetic macular edema, suggesting its potential role in early detection of therapeutic efficacy or failure. In this book chapter, we will provide a clinical overview of mitochondrial dysfunction and its relevance in the pathogenesis across a spectrum of retinal disease states. We will discuss the rationale of flavoprotein fluorescence (FPF) quantification as a proxy for measuring retinal oxidative stress and current studies that have investigated its utility.