The aim of this study was to provide comprehensive understanding of phenolic compounds composition in roots (RO), non-flower shoots (NFS) and flower shoots (FS) of Hypericum perforatum wild-growing plants from the Republic of Macedonia. Identification of phenolic compounds in plant methanolic extracts was performed by HPLC-DAD/ESI-MS analysis. Chlorogenic acid and 3-p-coumaroylquinic acid were identified in NFS and FS, while 3-feruloylquinic acid was detected in RO and FS extracts. From the group of flavan- 3-ols, (epi)catechin and procyanidins were found in all tested samples, whereas catechin and B-type procyanidin dimer were confirmed in NFS and FS. Four flavonol glycosides (hyperoside, rutin, quercitrin and kaempferol 3-O-rutinoside) were identified in aerial parts. Guaijaverin and kaempferol 3-O-glucoside were exclusively found in NFS. Quercetin, amentoflavone and I3-II8 biapigenin as flavonoid aglycones were detected only in FS extracts. The NFS and FS extracts showed a capability for the accumulation of cyanidin 3-O-glycoside and cyanidin 3-O-rhamnoside, as well for hyperforin and adhyperforin. Naphthodianthrones were represented with pseudohypericin, hypericin and  protopseudohypericin  in  FS, while only hypericin was detected in NFS. Six xanthones, γ-mangostin, 5-O-methyl-2- deprenylrheediaxanthone B, garcinone C, 3,6-dihydroxy-1,5,7-trimethoxy-xanthone, cadensin G and cadensin C were exclusively confirmed in RO extracts. Padiaxanthone was detected in NFS, while dimethylmangiferin in FS extracts. The major finding of this study is the identification of novel xanthones in H. perforatum roots that could be potentially used as bioactive compounds in food and pharmaceutical industry.