Many biochemical processes exploit the extraordinary versatility of flavoenzymes and their flavin cofactors. Flavoproteins are now known to have a variety of folding topologies but a careful examination of their structures suggests that there are recurrent features in their catalytic apparatus. The flavoenzymes that catalyse dehydrogenation reactions share a few invariant features in the hydrogen-bond interactions between their protein and flavin constituents. Similarly, the positioning of the reactive part of the substrate with respect to the cofactor is generally conserved. Modulation of substrate and cofactor reactivity and exact positioning of the substrate are key elements in the mode of action of these enzymes.