To analyse scientifically the fundamental formulation theory and drug interaction of Chungpegagan-tang, the extraction level of puerarin and daidzin, the transforming activity of puerarin and daidzin to daidzein by human intestinal bacteria and in vitro cytotoxicity against tumor cell lines of Chungpesagan-tang were investigated. When Puerariae Radix was extracted with Chungpesagan-tang composing herbal medicines, the puerarin extraction level from these polyprescriptions was decreased by the extraction with Raphani Semen or Cimicifugae Rhizoma, but the other herbal medicines increased it. The activity transforming puerarin and daidzin to daidzein by human intestinal bacteria was increased by Raphani Semen, Cimicifugae Rhizoma and Angelicae Tenuissimae Radix, but decreased by Scutellariae Radix and Rhei Rhizoma. Puerariae Radix did not showed in vitro cytotoxicity against tumor cell lines. However, by its anaerobic incubation with human intestinal bacteria, it showed a potent cytotoxicity. When the main components, puerarin and daidzin, of Puerariae Radix were incubated with human intestinal bacteria, the main metabolites were daidzein and calycosin. These metabolites had the most potent cytotoxicity, compared to those of puerarin and daidzin. Raphani Semen, Rhei Rhizoma and Chungpesagan-tang had also the potent cytotoxicity against tumor cell lines by the anaerobic incubation with human intestinal bacteria.