Flaxseed is considered an indispensable generally recognized as safe (GRAS) source of polyphenolic lignans, polyunsaturated fatty acids (PUFA), fibers as well as minerals and vitamins. The metabolite content of flaxseed reflects its nutritional and medicinal value. Therefore, the selection of flaxseed variety for food industry is dependent on its metabolome. A metabolomics approach based on liquid or gas chromatography coupled to mass spectrometry has been applied to discriminate different flaxseed cultivars that are commercially available in Egypt. The available Sakha cultivars were subjected to a comprehensive metabolomics and lipidomics approach for investigation of their metabolomes. Our results showed that among the screened cultivars, Sakha 6, with its yellow-colored testa, showed marked metabolic discrimination. This yellow cultivar showed high accumulation of essential amino acids. Additionally, the oil of this cultivar accumulated the highest content of the two essential PUFA: alpha-linolenic acid (an ω -3 fatty acid) and linoleic acid (an ω -6 fatty acid). Interestingly, the content of the main antinutritional cyanogenic glycosides such as linustatin and neolinustatin was lower, while, the content of medicinally-important secondary metabolites was higher in Sakha 6 cultivar. These results support the use of this cultivar for human consumption owing to its high nutritional and medicinal value.