The Cyto-ID® hypoxia/oxidative stress detection kit, together with the Mito-ID® O2 and pH sensor assays, may be used to profile hypoxia, reactive oxygen species, and mitochondrial dysfunction related to oxidative stress. With Cyto-ID, two membrane-permeable, fluorogenic probes simultaneously detect hypoxia and reactive oxygen species in live cells. The kit is suitable for analysis of suspension or adherent cells by fluorescent microscopy or flow cytometry. The companion assays may be used to assess mitochondrial oxygen consumption and to monitor cellular acid extrusion resulting from mitotoxicity-associated increases in glycolytic flux.