AbstractBACKGROUNDWatercore is a physiological disorder affecting fruit of some apple (Malus domestica Borkh.) cultivars. Intercellular spaces are filled with fluid, which reduces intercellular air space volume. In this study individual phenolic content, sugars and organic acids in watercore affected flesh have been identified and quantified. Peroxidase activity was also measured, as a potential stress indicator. The study was performed on three cultivars prone to watercore development ‘Delicious’, ‘Gloster’ and ‘Fuji’.RESULTSTotal phenolic content was higher in flesh of fruit without watercore in all three cultivars, which was mainly due to higher individual and total flavanol content. In contrast, total and individual dihydrochalcone content was higher in watercore flesh, where it was up to 2.4 times higher from the flesh of fruit without watercore. Also, peroxidase activity was higher in watercore flesh.CONCLUSIONHigher peroxidase activity and total and individual dihydrochalcone content leads us to believe that oxidative stress occurred. These results show that watercore has an influence on apple fruit sugar and phenol content even before any visual signs of internal breakdown and browning. With the development of non‐destructive techniques for phenol content determination, the knowledge about phenolic changes in watercore affected fruits could aid with apple fruit sorting. © 2015 Society of Chemical Industry