Cordyceps militaris (CM) has been used as antidiabetics, anticancer, endocrine and sexual functions enhancement in the traditional medicine. Water soluble fractions of CM showed cytotoxic activities on the three kinds of human cancer cell lines, stomachic adenocarcinoma(SNU-1), colorectal adenocarcinoma (SNU-C4), and hepatocellular carcinoma(SNH-354). Cytotoxic activity guided isolation and identification of active fractions afforded cordycepin as an active component.