The objective of the current study was to identify and quantify endogenous phenolic compounds in easy-to-root M.9 and M.26 rootstocks and difficult-to-root cultivars 'Hongro' (HR) and 'Fuji' (FJ) (scions) of apple (Malus domestica Borkh.) during in vitro rooting of shoots for 40 days in culture. Phloretic acid, coumaric acid, salicylic acid, chlorogenic acid, catechin hydrate, hesperetin, rutin, quercetin, and biochanin were the major endogenous phenolic compounds detected in the apple shoots by high-performance liquid chromatography (HPLC). Among the various phenolic compounds, chlorogenic acid was most abundant in shoots, favoring the induction and growth of adventitious roots from in vitro shoots. In contrast, salicylic acid was another phenolic acid that was reduced during the culture of shoots in the easy-to-root rootstocks (M.9 and M.26). However, salicylic acid levels remained constant or increased throughout the culture in the difficult-to-root cultivars (HR and FJ). This study indicates the role of endogenous phenolic compounds on the rooting of shoots and lays the foundation for further studies investigating the mechanism of rooting in these apple rootstocks and cultivars.