The aim of this PhD thesis was to evaluate the response of apple fruits (Malus domestica Borkh.) to selected physiological disorders (sunburn, watercore, bitter pit and scald) through metabolite analysis. Additionally, gene expression and enzyme activity of phenylpropanoid and flavonoid pathway plus polyphenol oxidase (PPO) and peroxidase (POX) activity were determined for certain disorders. Metabolites were analysed using UV-VIS, HPLC and HPLC-MS, gene expression with RT-qPCR and enzyme activities with UV-VIS and radiographic TLC scan. The response of apple fruits to different physiological disorders was not uniform. The affected tissues from all physiological disorders except watercore had higher contents of hydroxycinnamic acids. Generally higher contents of phenolic compounds were observed in the pits of bitter pit, whereas peels above the pit contained lower amounts of anthocyanins and flavonols. The latter were strongly increased in sunburned peels. One of the most notable results and yet least researched responses was the content of dihydrochalcones in connection to physiological disorders. Their content was higher in sunburned peels, flesh with watercore and in the pits of bitter pit in comparison to unaffected tissue. The P2'GT enzyme activity was also higher in the flesh of apples with watercore in comparison to flesh of apples without watercore. No statistically significant differences were observed in the activity of the rest of the enzymes of phenylpropanoid and flavonoid pathway (PAL, CHS/CHI, FHT, FLS in F3’GT) between treatments. Watercore incidence is reflected in the apple peel, which could aid in developing cost-efficient methods of fruit sorting. The most unequal response to physiological disorders was in the group of flavanols. Higher gene expression (MdCHS, MdCHI, MdFHT, MdANS and MdUFGT) was observed with scald development, but was not reflected in enzyme activity (PAL, FHT, CHS/CHI and DFR). Higher activity of POX was determined in flesh affected with watercore and sunburned peel, whereas it was lower in peel affected with scald in comparison to unaffected tissues. Comparing to unaffected tissues, PPO activity was higher in flesh with watercore and peel with scald.