Silibinin is an herbal polyphenol with high antioxidant and anticancer properties. In this study, its influence on U-CH2 (human sacral chordoma cell line) and MCF-7 (human breast adenocarcinoma cell line) cells was investigated and compared. We analyzed real-time cell viability by xCELLigence system. It was found that the cytotoxic effect of silibinin began about 10 hours after administration. Silibinin differentially influenced MCF-7 and U-CH2 cells and caused decrease in the cell index value of MCF-7 cells more than U-CH2 cells (more than 2 times) at 24 h. This suggests that silibinin is a promising drug for breast cancer but less favorable for chordoma.