In this study, after the treatment of shikonin or topotecan on the GSCs as well as glioma cells for 24 h, the expression of Bcl-2 protein significantly decreased, meanwhile the cleaved caspase-9 and cleaved caspase-3 proteins increased to a higher level, which indicated that inhibition of Bcl-2 protein with activation of caspase 9/3-dependent pathway was involved in shikonin or topotecan induced apoptosis process. The gene discussed is CASP9; the disease is central nervous system cancer.