The lipoxygenase gene family can synthesize an array of chiral hydroperoxy derivatives from polyunsaturated fatty acids. An individual enzyme, however, reacts molecular oxygen on a single position on the carbon chain and in a single stereo configuration. Regiospecificity is regulated by the orientation and depth of substrate entry into the active site. Stereospecificity is a different issue and only recently has experimental support emerged to explain the conceptual basis of stereo control. A key determinant is a single active site residue conserved as an Ala in S lipoxygenases and a Gly in R lipoxygenases; this residue controls R or S stereochemistry by switching the position of oxygenation on the reacting pentadiene of the substrate. In this review, we meld together the factors that control product regio- and stereochemistry into a general model that can account for the specificity of individual lipoxygenase reactions.