Seeds of Hypericum perforatum and H. tetrapterum were extracted with dichloromethane and methanol and investigated by chromatographic and mass spectrometric methods. Both species yielded a fatty oil fraction amounting to 30.5% and 18.0% of the seed weight, respectively. Linoleic acid (C18:2n-6) was shown to be the predominant fatty acid constituent. Moreover, xanthone derivatives, i.e. tetrahydroxyxanthones (THX), xanthone-glycosides and xanthone-sulfonates, were assigned in methanolic extracts. For structure elucidation, one representative xanthone, namely 1,3,6,7-THX, was synthesized and analyzed via HPLC-DAD/MS and GC/MS. Total THX contents were quantitated applying a validated HPLC-DAD method, resulting in 1.25 g/kg (H. perforatum) and 0.27 g/kg (H. tetrapterum), respectively. Moreover, the free radical scavenging capacity of the methanol extracts was tested using the DPPH antioxidant assay. Both, H. perforatum (IC = 8.7 mg/l) and 1,3,6,7-THX (IC = 3.0 mg/l), exhibited good DPPH free radical scavenging activity compared to Trolox (IC = 6.6 mg/l).