The effect of weather conditions and eleven apple rootstocks was studied on the phenol content in fruits. Superdwarf rootstocks P 61 and P 22 determined the highest content of all phenolic compounds tested. Dwarf rootstocks M.9, P 62 and semi-dwarf M.26 determined lower content of all phenolic compounds tested. The content of (+)-catechin, procyanidin B1 and total procyanidins content in apple fruits depended on rootstock genotype and high variation coefficient of these compounds between rootstocks was established. Rootstocks had a lesser effect on the content of quercitrin, (-)-epicatechin, total catechins, phloridzin and chlorogenic acid. No clear differences were found between super-dwarf, dwarf and semi-dwarf rootstock groups. Conditions during the growing season, yield and fruit weight impacted on the content of bioactive compounds. Less than 10% difference in total phenols between the growing seasons was recorded for M.26 and P 22. The greatest differences were recorded in the fruits from trees grown on M.9, Pure 1 and P 66 rootstocks. Rootstock B.396 determined the most stable content of all compounds analysed, except for procyanidin B1 and B2.