Two secoisolariciresinol diglucoside (SDG) diastereomers were extracted from flaxseed and liberated through alkaline hydrolysis. Anion-exchange and reversed-phase chromatography were successfully employed to purify the hydrolyzed flaxseed extract. On-line LC-NMR-MS analyses revealed the structure of the isolated and purified SDG diastereomers, [2R,2'R]-2,3-bis[(4-hydroxy-3-methoxyphenyl)-methyl]-1,4-butanediyl-bis-beta-glucopyranoside the predominant flaxseed lignan and [2R,2'S]-2,3-bis[(4-hydroxy-3-methoxyphenyl)methyl]-1,4-butanediyl-bis-beta-glucopyranoside, a previously incompletely characterized minor flaxseed lignan. Circular dichroism (CD) analyses confirmed the presence of two distinguished optically active compounds present in the flaxseed extract.