High-speed counter-current chromatography was successfully used for the isolation and purification of secoisolariciresinol diglucoside, a bioactive lignan from flaxseed (Linum usitatissimum L.). The solvent system consisted of tert.-butylmethyl ether-n-butanol-acetonitrile-water (1:3:1:5). The purity and identity of the isolated compound was checked by high-performance liquid chromatography analysis in combination with mass spectrometry and NMR measurements.