The ethanol extract of Geranium carolinianum L., a domestic plant grown in China, was subjected to sequential extractions with different organic solvents. The extracts were assayed for anti-hepatitis B virus (HBV) activities. The ethyl acetate fraction was found to contain the highest level of anti-HBV activity. In order to identify the active ingredients, the ethyl acetate fraction was further fractionated by column chromatography. Seven compounds were identified including ellagic acid, geraniin, quercitrin, hyperin, hirsutrin, quercetin, and kaempferol, whose structures were determined by NMR. The presence of the anti-HBV compounds geraniin, ellagic acid and hyperin in G. carolinianum L. may account for the effectiveness of this folk medicine in the treatment of HBV infections. Geraniin inhibited hepatitis B surface antigen (HBsAg) and hepatitis B e antigen (HBeAg) secretion by more than 85.8% and 63.7%, respectively, at the non-cytotoxic concentration of 200 microg/ml. The inhibitions of HBsAg and HBeAg secretion by geraniin were higher than the inhibition by the positive control Lamivudine, 33.5% and 32.2% respectively, at the same concentration. Since HBeAg is involved in immune tolerance during HBV infection, the newly identified anti-HBV compound geraniin might be a candidate agent to overcome the immune tolerance in HBV-infected individuals. This is the first report of the anti-HBV effects of geraniin and hyperin, the active substances derived from G. carolinianum L.