Compositional changes of skin and seed phenolic compounds and berry glycosylated aroma precursors were measured in Vitis vinifera L. cv. Cabernet Sauvignon onto 1103P and SO4 rootstocks, in three irrigation regimes (FI, 100% of evapotranspiration; DI, 50% of evapotranspiration; and NI, non-irrigated). The study was conducted in a commercial vineyard of central Greece, in a factorial experiment during two growing seasons (2005-2006). Grape samples were obtained at commercial harvest. The deficit water supply decreased berry size but did not affect the skin/pulp weight ratio. Water limitation, especially pre-veraison, caused a substantial increase of skin anthocyanin concentration, and this effect was independent of water deficit-induced reductions in berry size and vine vigor. Among individual anthocyanins, malvidin-3-O-glucoside was mostly affected by water supply. The rootstock genotype did not affect berry growth parameters and skin polyphenol concentrations. The irrigation regime (mainly post-veraison) and rootstock genotype affected total flavan-3-ol monomers in seed tissue, mainly as a result of variations in the catechin amount. The lower seed phenolic concentration was found in non-irrigated and SO4-grafted vines, probably as a result of the restriction of scion vigor caused by these treatments, thereby altering cluster exposure. Skin and seed tannins were not affected by either rootstock or irrigation. The limited water supply was associated with increased aroma potential at harvest.