The positive effect of lipoxygenase, added as an enzyme-active soy flour, during the production of white bread is well established. In addition to increasing the mixing tolerance and overall dough rheology, lipoxygenase is also an effective bleaching agent. It is known that these effects are mediated by enzyme-coupled cooxidation of gluten proteins and carotenoids. However, the mechanism whereby these effects are achieved is not yet fully understood. In order to gain a better understanding into the reactions governing the beneficial effects of lipoxygenases in bread dough, an in-depth knowledge of the lipoxygenase catalytic mechanism is required. Until now no single review combining the molecular enzymology of lipoxygenase enzymes and their application in the baking industry has been presented. This review, therefore, focuses on the extraction and molecular characterization of lipoxygenases in addition to the work done on the application of lipoxygenases in the baking industry.