Common buckwheat (Fagopyrum esculentum Moench) is a valuable source of proteins, B vitamins, manganese, tryptophan, phytochemicals with an antioxidant effect, and the natural flavonoid rutin. Due to its composition, buckwheat supports the human immune system, regulates blood cholesterol, and is suitable for patients with diabetes or celiac disease. The study aimed to compare the allocation of selected phenolic acids (neochlorogenic acid, chlorogenic acid, trans-caffeic acid, trans-p-coumaric acid, trans-sinapic acid, trans-ferulic acid) and flavonoids (rutin, vitexin, quercetin, kaempferol) in the leaves, flowers, and grain of buckwheat cultivars of different origin. The content of individual phenolics was determined by the HPLC-DAD method. The results confirmed the determining role of cultivar on the relative content of chlorogenic acid, trans-caffeic acid, trans-sinapic acid, vitexin, and kaempferol in buckwheat plants. A significantly negative correlation among concentrations of phenolic acids in different common buckwheat plant parts shows that there are different mechanisms of genetic influences on the concentration of phenolic substances in common buckwheat flowers, leaves, and grain. These differences should be taken into account when breeding buckwheat for a high concentration of selected phenolic substances.