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Phenolic compounds are plant secondary metabolites, one of the most common and widespread groups of substances in plants, as well as a major group of phytochemicals present in medicinal and aromatic plants. The phytochemical composition of the hydroalcoholic extracts from <i>S. raeseri</i>, <i>S. scardica</i> and <i>S. syriaca</i> was determined by LC-MS/MS-QTOF analysis. A total amount of 23 secondary metabolites were identified, including 17 flavonoids (Fs), 4 phenylethanoid glycosides (PEGs), 1 phenolic acid (PA) and 1 fatty acid (FA). Among the three species, the constituents that have been detected in all of nine samples were: verbascocide/isoverbascoside (PEG), apigenin 7-<i>O</i>- glucoside (F), isoscutellarein 7-<i>O</i>-[6″-<i>O</i>-acetyl]-allosyl(1→2)-glucoside (F) and apigenin 7-(4″-<i>p</i>-coumaroylglucoside) (F). This study contributes to the phytochemical characterization of the <i>Sideritis</i> spp. by providing a comparative study of bioactive compounds present in three different <i>Sideritis</i> species, <i>S. raeseri</i>, <i>S. scardica</i> and <i>S. syriaca</i>, which are widely used as a herbal medicine in Mediterranean region and Balkan Peninsula.