Lipoxygenases convert polyunsaturated fatty acids into a number of chiral hydroperoxides, which are involved in different biological pathways. We applied the exciton‐coupled circular dichroism (ECCD) method to determine the absolute configuration of acyclic hydroxylated dienes derived from the lipoxygenase catalyzed dioxygenation of 1(Z),4(Z)‐unsaturated fatty acids. The CD spectra of the 2‐naphthoate derivatives of reduced hydroperoxides reveal, depending on R or S configuration of the hydroxyl group, a negative or positive chiral twist between the 2‐naphthoate chromophore and the diene chromophore in the molecule. Thus, lipoxygenase stereoselectivity can be deduced from a single CD measurement. Chirality 9:563–567, 1997. © 1997 Wiley‐Liss, Inc.