A specific ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) method was developed for the simultaneous determination of puerarin, daidzein, baicalin, wogonoside and liquiritin in rat plasma. Chromatographic separation was performed on a C(18) column packed with 1.7 microm particles by a linear gradient elution. The analytes and carbamazepine (internal standard, I.S.) were monitored in a selected-ion reaction (SIR) mode with a positive electrospray ionization (ESI) interface by the following ions: m/z 417.2 for puerarin, m/z 255.2 for daidzein, m/z 271.0 for baicalin, m/z 461.0 for wogonoside, m/z 441.0 for liquiritin and m/z 237.2 for carbamazepine (I.S.), respectively. The calibration curves of these analytes were linear over the concentration ranges from 0.00254-1.02 microg mL(-1) to 0.0102-10.2 microg mL(-1). Within-batch and between-batch precisions (RSD%) were all within 15% and accuracy (RE%) ranged from -10% to 10%. The extraction recoveries were on average 79.8% for puerarin, 90.8% for daidzein, 74.4% for baicalin, 70.2% for wogonoside and 84.7% for liquiritin. The validated method was successfully applied to investigate the pharmacokinetics of five bioactive compounds of GegenQinlian decoction (GQD) in rats.