The dichloromethane extract of the roots and heartwood of Caesalpinia sappan exhibited potent inhibitory activity against β-hexosaminidase release as marker of degranulation in rat basophilic leukemic (RBL-2H3) cells, with inhibition of 98.7% and 87.5% at concentration of 100 µg/ml, respectively. These extracts were further separated by chromatographic techniques to give two chalcones and seven homoisoflavones. Among the compounds tested, sappanchalcone (2) possessed the most potent effect against allergic reaction in RBL-2H3 cells with an inhibitory concentration (IC50) value of 7.6 µM, followed by 3-deoxysappanchalcone (1, IC50 = 15.3 µM), whereas other compounds showed moderate and mild effects. The results suggested the following structural requirements of chalcones (1 and 2) and homoisoflavones (3-9) for anti-allergic activity: (i) chalcone exhibited higher activity than homoisoflavone (ii) vicinal hydroxylation at B-ring of chalcone conferred higher activity than one hydroxylation; and (iii) for homoisoflavone, the hydroxyl groups at C-3 and C-4 positions decreased the activity. This is the first report of C. sappan for anti-allergic activity. Copyright © 2009 John Wiley & Sons, Ltd.