The article addresses the issues of using metabolomic analysis to study genetic resources of cereal crops in order to (1) determine phylogenetic linkages between species (the degree of domestication); (2) within species to describe genetic diversity according to its responses to biotic and abiotic stressors and biochemical characteristics (chemical compounds) determining food, feed and technological quality indicators; and (3) select the most resistant and highest-quality genotypes for complex breeding use.