The initial steps in the autoxidation of CLA methyl ester are poorly understood. The aim of this study was to determine the stereochemistry of the hydroperoxides formed during autoxidation of CLA methyl ester in the presence of a good hydrogen atom donor. For this purpose, 9-cis,11-trans CLA methyl ester was autoxidized in the presence of alpha-tocopherol under atmospheric oxygen at 40 degrees C in the dark. The CLA methyl ester hydroperoxides were isolated, reduced to the corresponding hydroxy derivatives, and separated by HPLC. The stereochemistry of seven hydroxy-CLA methyl esters was investigated. The position of the hydroxy group was determined by GC-MS. The geometry as well as the position of the double bonds in the alkyl chain was determined by NMR. In addition, the 13C NMR spectra of six hydroxy-CLA methyl esters were assigned using COSY, gradient heteronuclear multiple bond correlation, gradient heteronuclear single quantum correlation, and total correlation spectroscopy experiments. The autoxidation of 9-cis,11-trans CLA methyl ester in the presence of a good hydrogen atom donor is stereoselective in favor of one geometric isomer, namely the 13-(R,S)-hydroperoxy-9-cis,11-trans-octadecadienoic acid methyl ester. Three types of conjugated diene hydroperoxides are formed as primary hydroperoxides: trans,trans hydroperoxides (12-OOH-8t,10t and 9-OOH-10t,12t), a cis,trans hydroperoxide with the trans double bond adjacent to the hydroperoxide-bearing carbon atom (13-OOH-9c,11t), and a new type of cis,trans lipid hydroperoxide with the cis double bond adjacent to the hydroperoxide-bearing carbon atom (8-OOH-9c,11t). In addition, three nonkinetic hydroperoxides (13-OOH-9t,11t, 8-OOH-9t,11t, and 9-OOH-10t,12c) are formed. This study supports the theory that CLA methyl ester autoxidizes at least partly through an autocatalytic free radical reaction. The complexity of the hydroperoxide mixture is due to formation of two different pentadienyl radicals. Moreover, the stereoselectivity in favor of one geometric isomer can be explained by the selectivity of the two previous steps: the preferential formation of a W-conformer of the pentadienyl radical over the Z-conformer, and regioselectivity of the oxygen addition to the pentadienyl radical.