Crude extracts of callus and roots of Dipteryx odorata were analyzed by HPLC to detect and quantify isoflavone contents. Based on spectroscopic and X-ray crystallography data the structures of two isoflavones were elucidated as 7-hydroxy-4',6-dimethoxyisoflavone and 3',7-dihydroxy-4',6-dimethoxyisoflavone. The production of dry biomass of 7-hydroxy-4',6-dimethoxyisoflavone in cultured callus was 4.12 mg/g, approximately eleven fold higher than the amount accumulated in roots of D. odorata wild-growing plants. The 7-hydroxy-4',6-dimethoxyisoflavone was effective against glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma cruzi. This is the first report on those bioactive isoflavones accumulated in callus of D. odorata.