Flavinium salts, both isoalloxazinium and alloxazinium derivatives, are useful organocatalysts of redox reactions, and particularly in recent years, the number of transformations catalysed by flavinium salts has increased. This review outlines the synthetic applications of flavinium catalysts in oxygenation reactions with oxygen and hydrogen peroxide as terminal oxidising agents; these oxidations involve flavin hydroperoxide as an intermediate, thus mimicking flavin monooxygenases. Special attention is paid to mechanistic studies and to the design of catalytic systems, especially the effects of the structures of flavinium catalysts, and reaction conditions on the efficiency, chemoselectivity and stereoselectivity of oxygenations.