Liquid chromatography coupled to diode array and electrospray ionization mass spectrometry detection was used to establish the polyphenolic profile of an ethyl acetate fraction from Agrimonia eupatoria L. aqueous-alcoholic extract. Additionally, an HPLC technique with post-column derivatization by p-dimethylaminocinnamaldehyde was employed for the selective detection and quantification of flavan-3-ols. Important information was obtained by combining the data of these two HPLC techniques. Flavan-3-ols (catechin and procyanidins B1, B2, B3, B6, B7, C1, C2 and epicatechin-epicatechin-catechin), quercetin 3-O-glucoside, quercetin 3-O-galactoside, kaempferol 3-O-glucoside, kaempferol 3-O-(6''-O-p-coumaroyl)-glucoside, apigenin 6-C-glucoside and various phenolic acids were identified. Antioxidant activity of the Agrimonia eupatoria L. fraction containing these compounds was assessed through the 1,1-diphenyl-2-picrylhydrazyl, trolox equivalent antioxidant capacity and thiobarbituric acid reactive substances methods. Significant activity was observed for this fraction, where compounds with recognized antiinflammatory properties such as procyanidins, kaempferol 3-O-(6''-O-p-coumaroyl)-glucoside and quercetin glycosides were identified for the first time. These results are predictive of the beneficial effects of this fraction, or some of its compounds, in human health, as possible anti-inflammatory drug.