Shuang-Huang-Lian (SHL) is a traditional Chinese formula containing Lonicerae japonicae flos (LJF), Scutellariae radix (SR) and Forsythiae fructus (FF), and is commonly used to treat acute upper respiratory tract infection, acute bronchitis and light pneumonia. The aim of this study is to compare the pharmacokinetics of SHL and the different combinations of its constitutional herbs, and to investigate the influence of compatibility on the pharmacokinetics of the main active ingredient baicalein. Male Sprague-Dawley rats were randomly assigned to four groups and orally administered with SHL, SR, SR+FF and SR+LJF, respectively. At different time points (0, 0.167, 0.333, 0.5, 0.75, 1, 3, 5, 8, 12, 18, 24, 36, 48, 72 h) after administration, the concentrations of baicalein in rat serum were determined by using HPLC, and main pharmacokinetic parameters were estimated. It was found that there were significant differences (p < 0.05) in the parameters, t(1/2) (beta) and C(max) among different combinations of herbs. The results indicate that SHL has delayed the elimination and reduced the bioavailability of baicalein in rat serum.