Cnidii monnieri Fructus [CmF; Cnidium monnieri (L.) Cusson] is used as a tonic agent in traditional Chinese medicine. In a previous Chinese herb-cytotoxicity screening test, the ethanol extract of CmF exhibited strong effects on human leukemia (HL60), cervical carcinoma (HeLa) and colorectal carcinoma (CoLo 205) cells. Then, the CmF extract was subjected to silica gel column chromatography and recrystallization to give five coumarins: osthol, imperatorin, bergapten, isopimpinellin, and xanthotoxin. Among these compounds, osthol showed the strongest cytotoxic activity on tumor cell lines. The structure-activity relationship established from the results indicated that the prenyl group has an important role in the cytotoxic effects. However, imperatorin showed the highest sensitivity to HL-60 cells and the least cytotoxicity to normal PBMCs. Osthol and imperatorin both caused apoptotic bodies, DNA fragmentation, and enhanced PARP degradation in HL-60 cells by biochemical analysis. These results indicate that osthol and imperatorin can induce apoptosis in HL-60 cells. Therefore, osthol and imperatorin are cytotoxic marker substances in the fruits of Cnidium monnieri.