Using a validated high-performance liquid chromatographic (HPLC) method, the pharmacokinetics of multi-constituents in Huangqin-Tang decoction were simultaneously studied both in the compound prescription and in each single herb decoction. At different intervals (0, 1, 2, 4, 8, 12, 24, 36, 48 h) after oral administration of the Huangqin-Tang decoction or a single herb decoction at a dose of 10 g x kg(-1), the concentrations of the constituents and their metabolites: baicalin (BG), wogonoside (WG), oroxylin-A-glucuronide (OG), baicalein (B), wogonin (W), oroxylin-A (O), paeoniflorin (PF), paeonimetabolin-I (PM-I), liquiritin (LG), liquiritigenin (L), glycyrrhizic acid (GL) and glycyrrhetinic acid (GA), were detected in the rat plasma. A new metabolite-3,5,7,2',6'-penta hydroxy flavone (visidulin I, VD-I) was found in rat plasma after oral administration of Huangqin-Tang or a single herb Huangqin decoction, and the quality was identified by HPLC and LC/MS. The pharmacokinetic parameters of the constituents and metabolites in the compound prescription and single herb decoctions were compared. All concentration-time curves corresponded to the one-compartment model. The constituents of BG, WG, OG, VD-I and LG had higher C(max) and AUC(0-lim) in the compound prescription than in the single herb decoction, and WG had significant difference. The constituents of PF, W and O only had a higher AUC(0-lim) in the compound prescription, and O had a significant difference. It was concluded, in brief, that there were obvious differences in the pharmacokinetic parameters of most constituents (especially constituent WG) between the compound prescription and single herb decoction. The constituents in the compound prescription had delayed absorption and elimination, a longer residence time in the body, and higher C(max) and AUC(0-lim), than those in the single herb decoction. Therefore, they were more efficient and durable, making them promising to exerting pharmacological effects in vivo.