Understanding the biology of breast cancer stem cells and trying new ways to obliterate these cells would be a key step in developing cures for breast cancer. The objective of this study was to investigate the effect of mutant TNFα on human breast cancer stem cells derived from MCF7 cell line under the characterization of biologic features of these cells in vitro. By FACS analysis and sorting, we got MCF7 side population (SP) cells and showed that MCF7 SP cells possess cancer stem cell characteristics using the accepted breast cancer stem cell markers, but do not express multiple drug resistance transporters. Furthermore, by RT-PCR, these stem cells were found to constitutively express TNFR-p55 and TNFR-p75. After being treated with Mt rh471 TNFα, SP cells displayed a decreased self-renewal ability and an increased apoptosis by three different methods. When monocolony antibody against TNFR-p55 was added into the culture medium, the inhibitory effect of Mt rh471 TNFα on self-renewal was blocked completely, but this was not the case for that of Wt rhTNFα. The possible reasons might be that the increased binding of Mt rh471 TNFα mainly to TNFR-p55 results in induction of apoptosis of SP cells, while Wt rhTNFα could bind to both TNFR-p55 and TNFR-p75 which would lead to NFkB activity, resulting in a discounted apoptotic effect. These data suggest that Mt rh471 TNFα might be a negative regulator of the breast cancer stem cell-like cells and have the potential to treat breast cancer in clinic.