Quinones are abundant cyclic organic compounds present in the environment as well as in pro- and eukaryotic cells. Several species have been shown to possess enzymes that afford the two-electron reduction to the hydroquinone form in an attempt to avoid the generation of one-electron reduced semiquinone known to cause oxidative stress. These enzymes utilize a flavin cofactor, either FMN or FAD, to transfer a hydride from an electron donor, such as NAD(P)H, to a quinone substrate. This family of flavin-dependent quinone reductases shares a flavodoxin-like structure and reaction mechanism pointing towards a common evolutionary origin. Recent studies of their physiological functions in eukaryotes suggest a role beyond detoxication of quinones and involvement in the oxygen stress response. Accordingly, mammalian quinone reductases emerge as central molecular switches that control the lifespan of transcription factors, such as p53, and hence participate in the development of apoptosis and cell transformation.