15-Lipoxygenases are lipid-peroxidizing enzymes which have been implicated in the pathogenesis of various diseases, such as inflammation, atherosclerosis, and osteoporosis. Although the crystal structures for several lipoxygenase isoforms have been solved, there is little information on the substrate alignment at the active site and its impact on the catalytic mechanism. Investigating the oxygenation of specifically designed hydroxy fatty acids, we observed a pronounced enantioselectivity of 15-lipoxygenases for substrates carrying the oxygen moiety in close proximity to the site of hydrogen abstraction [16(R/S)-HETE, 17(R/S)-HETE]. To investigate the mechanistic basis for this unexpected behavior, we applied a strategy involving targeted substrate modification, site-directed mutagenesis, and structural modeling of the enzyme-substrate complex. Taken together, our data suggest that an (S)-hydroxy group in 16-HETE may form a hydrogen bridge between the substrate molecule and Gln548, which contributes to proper alignment of the fatty acid derivative at the active site of the enzyme. This interaction, which was not observed with 16(R)-HETE, 18(R)-HETE, or 18(S)-HETE, appears to be a major reason for the high degree of enantioselectivity during lipoxygenation of 16-HETE.