Twenty-one samples of Sideritis species (S. scardica, S. raeseri, S. taurica, S. syriaca and S. perfoliata) from various locations on the Balkan Peninsula were evaluated for their chemical constituents. Chemical analyses were focused on secondary metabolites, particularly phenolic compounds, which have several roles in the plant physiological processes and have demonstrated significant health beneficial effects. The occurrence of hydroxycinnamic acids, phenylethanoid glycosides and flavonoids has been investigated in taxonomically related taxa of the genus Sideritis. A systematic method for phenolic compounds identification was developed using tandem mass spectrometry coupled to high performance liquid chromatography with diode array detection. Scanning for precursor ions of commonly found phenolics in Sideritis species using LC/MS11 with an ion trap instrument permitted the specific determination of hydroxycinnamic acid derivatives, and phenylethanoid and flavonoid glycosides. Further characterization of each phenolic compound was performed using MS/MS product-ion analysis and common-neutral-loss analysis. This on-line technique allowed identification of three hydroxycinnamic acid derivatives, eight phenylethanoid glycosides, and twenty-four flavonoid glycosides. All the taxa analysed produced very similar phenolic patterns characterized by the presence of 5-caffeoylquinic acid, lavandulifolioside, verbascoside, hypolaetin 7-O-[6'''-O-acetyl]-allosyl(1-->2)glucoside, apigenin 7-(4"-p-coumaroylglucoside), 4'-O-methylisoscutellarein 7-O-[6'''-O-acetyl]-allosyl(1-->2)glucoside, and minor amounts of isoverbascoside, apigenin 7-O-allosyl(1-->2)glucoside, isoscutellarein 7-O-allosyl-(1-->2)-[6"-O-acetyl]-glucoside, hypolaetin 7-O-allosyl-(1-->2)-[6"-O-acetyl]-glucoside and 4'-O-methylhypolaetin 7-O-[6'''-O-acetyl]-allosyl-(1-->2)-[6"-O-acetyl]-glucoside. These results show that the investigated species are systematically very closely related. Phenylethanoid glycosides and flavonoid acetylglycosides are dominant and constitute 90% of the total phenolic compounds compared with hydroxycinnamic acid and flavonoid 7-O-glycosides. Principal component analysis (PCA) was performed for the nature and content of the different compounds to be correlated to the particular Sideritis species and also to the locations.