Phenolic compounds were extracted from flaxseed using 80% (v/v) methanol. The resultant crude extract was hydrolysed under basic conditions. Secoisolariciresinol diglucoside (SDG) was separated from the prepared extract using semi-preparative HPLC. Secoisolariciresinol (SECO) was liberated from SDG by acid hydrolysis. The chemical structures of SDG and SECO were confirmed by ESI-MS. Capillary zone electrophoresis (CZE) was employed for separation of phenolics from the crude extract, the extract resulting after base hydrolysis, and the two lignans. CZE was found to offer a quicker analysis of SDG with higher separation efficiency than by a conventional HPLC methodology. The retention time for SDG was noted at 5.33 min. The migration times of SDG and SECO were close together; a base line separation of both lignans was not achieved. The electropherogram of the crude flaxseed extract showed only one broad peak with a retention time of 6.02 min.