Mitochondrial free radicals and redox poise are central to metabolism and cell fate. Their measurement in living cells remains a major challenge and their in vivo dynamics are poorly understood. Reports of 'superoxide flashes' in single mitochondria have therefore been perceived as a major breakthrough: single mitochondria expressing the genetically encoded sensor circularly permuted yellow fluorescent protein (cpYFP) display spontaneous flashes of fluorescence that are responsive to metabolic changes and stressors. We critically review the evidence that underpins the interpretation of mitochondrial cpYFP flashes as bursts of superoxide production and conclude that flashes do not represent superoxide bursts but instead are caused by transient alkalinisation of the mitochondrial matrix. We provide a revised framework that will help to clarify the interpretation of mitochondrial flashes.