The purpose of the study was to develop a new deep eutectic solvent-based microwave-assisted extraction (DES-MAE) method for extracting the three major active compounds genistin, genistein and apigenin from pigeon pea roots. Optimal conditions for DES-MAE, proposed by the single factor and the Box-Behnken design (BBD) tests, were 30% of water in 1,6-hexanediol/ChCl (7:1, mol/mol) as the extraction solvent, microwave power 600W, liquid/solid ratio 14 mL/g, temperature 80 degrees C and time 11 min. The yields of genistin, genistein and apigenin reached 0.449, 0.617 and 0.221 mg/g DW, respectively. The kinetics experiment showed the prominent advantages of DES-MAE such as higher extraction efficiency than other extraction methods. The present results showed that DES could be a kind of green solvent for fast and efficient extraction of the active ingredients from plant materials. (C) 2015 Elsevier B.V. All rights reserved.