The grains and sprouts of colored wheat genotypes (having blue, purple and yellow colored grains) contain specific anthocyanidins, such as pelargonidin and cyanidin derivatives, that produce beneficial health effects. The objective of the presented study is to compare the antioxidant capacity and contents of bioactive phytochemicals in grains and sprouts of wheat genotypes that differ in grain color. The methods α, α-diphenyl-β-picrylhydrazyl (DPPH) and 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) scavenging activities, together with spectrophotometrical and high-performance thin-layer chromatography (HPTLC) methods, were used to study the presence of total phenolics, flavonoids, anthocyanins and anthocyanidins (pelargonidin, peonidin, cyanidin, delphinidin) content. It was predicted that the sprouts of all colored wheat genotypes would have significantly higher total flavonoids, total phenolics, anthocyanidin levels and antioxidant activity than the grains. The correlation results between antioxidant activity and contents of bioactive phytochemicals in grains and sprouts of colored wheat genotypes have shown a high correlation for cyanidin and pelargonidin, especially in grains, as well as quercetin in sprouts. It was found that total anthocyanin, quercetin and pelargonidin contents were significantly higher in the sprouts of the purple wheat genotypes than in the blue or yellow wheat genotypes. Delphinidin was detected at a higher level in the grains than in the sprouts of the blue wheat genotypes. Peonidin was present at very low quantities in the grains of all colored wheat genotypes. The sprouts of the purple wheat genotypes, among the colored wheat genotypes, had the highest pelargonidin, cyanidin and quercetin contents and, therefore, can be a promising source for functional food use.