In the first step of apple juice production, phenolic compounds undergo enzymatic oxidation 7 leading to the formation of newly formed molecules. More information is needed concerning the concentrations of oxidized phenolic compounds (OP) in apple juices to better understand their contribution to organoleptic and nutritional properties. In this study, native and oxidized phenolic compounds were quantified in 54 commercial and experimental apple juices. HPLC-MS method was developed to quantify two families of OP (5-O-caffeoylquinic acid dehydrodimers and epicatechin-5-O-caffeoylquinic acid heterodimers). A statistical clustering analysis (Euclidian Ward’s method) was performed on all phenolic compounds data sets. These two series of oxidation products could represent more than 14% of the total phenolic compounds quantified (TPQ). To the best of our knowledge, it is the first time that both families of OP were successfully quantified in apple juices. These compounds exhibit original polyphenolic structures that may contribute to nutritional and organoleptic properties in the juices. Moreover, most of the experimental juices and some from local cider producers (mostly made from “cider apple varieties”), were on average eight times more concentrated in polyphenols than juices mainly found in supermarkets. These results underlined the importance of apple varieties on the polyphenol content of the juices.