Plant secondary metabolites anthocyanins are considered to play a protective role. In bread wheat (Triticum aestivum L.), anthocyanins can be observed in both adult plants and seedlings. The aim of the current study was to investigate the putative role of anthocyanins present in grains and shoots with respect to the protection of seedlings against drought. For this purpose a set of near isogenic lines (NILs) differing in pericarp and coleoptile colour was used. Water stress was created by artificial shortage of moisture under laboratory conditions. Differences among the lines were observed in a way that the lines with dark-purple grains and coleoptiles (genotype Pp-D1Pp-D1Pp3Pp3Rc-A1Rc-A1Rc-D1Rc-D1) demonstrated a higher seedling drought tolerance than plants with uncoloured pericarp and lightpurple coleoptiles (pp-D1pp-D1pp3pp3Rc-A1Rc-A1rc-D1rc-D1). Furthermore, protection of the root system and the shoot was related with the presence of anthocyanins in grains and coleoptiles, respectively.