Molecular biochromatography with alpha1-acid glycoprotein (AGP) stationary phase was proposed to screen and analyse the biologically active components in traditional Chinese medicines (TCMs) with extracts from Radix Salviae miltiorrhizae as a tested sample. More than ten peaks were resolved based on their affinity to AGP. The effects of concentrations of acetonitrile, pH, concentration of inorganic salt and temperature on the retention behaviors of several major active components were also investigated, and it was found that the hydrophobic effect is the major contributor to retention. Tanshinone IIA was identified as one of the principal bioactive components, which is the marker for the quality control of Radix Salviae miltiorrhizae and a complicated remedy named YiXiTongMai. The amount of tanshinone IIA in Radix Salviae miltiorrhizae and YiXiTongMai determined by this method was 2.9 mg/g (net weight, RSD 4.9%, n=5) and 0.078 mg/g (net weight, RSD 2.5%, n=3), respectively. The possibility for fast differentiation of the TCM sources was also studied by the comparison of the fingerprint of chromatograms for eight typical TCMs on the AGP column. It was observed that different TCMs showed different fingerprint characteristics. Even for the same plant, Rhizoma cimicifugae from three different geographical sources, although there were common characteristics, distinct differences in types and concentrations of biologically active components were clearly observed. It was shown that molecular biochromatography was an effective and fast way for the analysis and screening of biologically active compounds in traditional Chinese medicines.