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Four xanthones isolated from the roots of Andrographis paniculata were tested in vitro for antiprotozoal activity against Trypanosoma brucei brucei, Trypanosoma cruzi and Leishmania infantum. Compound TDR13011 (1,2‐dihydroxy‐6,8‐dimethoxy‐xanthone) showed good activity against T. b. brucei and L. infantum with a 50% inhibitory concentration (IC₅₀) of 4.6 µg/ml and 8 µg/ml respectively. Xanthones from the roots of Andrographis paniculata exhibited promising anti‐protozoal activity and these compounds could be chemically modified to obtain a more potent product. Copyright © 2008 John Wiley & Sons, Ltd.