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Background: Extracts of Hypericum perforatum L. (common St John's wort; Hypericaceae) are sold as phytopharmaceuticals and herbal supplements to treat mild to moderate depression and as food additives. Extensively cultivated in Europe, plants can be infected by anthracnose (Colletotrichum gloeosporioides), a virulent fungal pathogen that causes tissue necrosis and dramatically decreases crop value. Such infections triggered the production of new secondary metabolites, specifically xanthones, in cell culture experiments., Results: Bioassay-guided fractionation of H. perforatum root extracts, testing for growth inhibition of plant pathogenic fungi from the genera Colletotrichum, Botrytis, Fusarium and Phomopsis, was performed. In vitro anti-inflammatory activity through inhibition of COX-1, COX-2 and 5-LOX-catalyzed LTB(4) formation was also evaluated. Extracts were analyzed by various chromatographic means and structure elucidation was performed using data from nuclear magnetic resonance and mass spectrometry., Conclusion: Researchers have previously described constituents from the aerial parts of this species, but few reports describe secondary metabolites found in underground parts, of particular interest because the lower stem and upper root are often sites of fungal infection. This work resulted in the isolation of three xanthones: 1,6-dihydroxy-5-methoxy-4',5'-dihydro-4',4',5'-trimethylfurano-(2',3':3,4)-xanthone; 4,6-dihydroxy-2,3-dimethoxyxanthone; and cis-kielcorin, one of which possessed novel bioactivity against species of Phomopsis and inhibited 5-LOX-mediated LTB(4) formation., (2010 Society of Chemical Industry.)