In the first step of apple juice production (crushing and pressing), phenolic compounds undergo enzymatic oxidation, forming newly formed molecules. More information is needed concerning the concentrations of those oxidized phenolic compounds (OP) in apple juices to better understand their real contribution to organoleptic and nutritional properties. In this study, native phenolic compounds and oxidized phenolic compounds were quantified in 54 commercial and experimental apple juices. HPLC-MS method was specially developed and validated 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. Interestingly, 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 (CQA dehydrodimers and EC-CQA heterodimers) were successfully quantified in apple juices. Noticeably, these compounds exhibit very original polyphenolic structures that are not encountered in fresh apples and may contribute to specific nutritional and organoleptic properties in the juices. In addition, we noted that most of the experimental juices (made from “cider apple varieties”) and some juices from local cider producers (mostly made from “cider apple varieties”), were found to be on average eight times more concentrated in polyphenols than juices mainly found in supermarkets (mostly made from “dessert apples”). These results of experimental apple juices underlined the importance of apple varieties on the polyphenol content of the juices. In addition, the part of the phenolic compounds represented by the oxidized forms should not be neglected