Previous experimental natural abundance deuterium (NAD) NMR results have shown an odd/ even-related alternation in the (H-2/H-1) ratio of the methylene groups of fatty acids (ChemBioChem 2001, 2, 425) and, by NAD NMR in CLC, a marked difference between enantiotopic deuterons for each methylenic site (Anal. Chem. 2004, 76, 2827). However, to date, the assignment of the absolute configuration for each deuterium has not been possible. To investigate further the origin of these effects, the assignment of NAD quadrupolar doublets observed in chiral oriented solvent is required. Here we describe the assignment of R- and S-isomers resulting from the isotopic substitution in positions 4 and 5 in the aliphatic chain of 1,1'-bis( thiophenyl) hexane 1 (BTPH) derived from natural linoleic acid of plant origin. This was achieved using an optimized synthetic strategy to obtain separately four regio- and stereoselectively deuterated enantiomers of BTPH. By reference to the deuterium spectra of these isotopically labeled reference compounds, we demonstrate that, on both 4 and 5 positions of BTPH, the isotopic enantiomers of S configuration are depleted relative to those of R configuration. This finding effectively explains the observed low (H-2/H-1) ratio in NAD of some ethylenic sites of unsaturated fatty acids.