Objective To summarize the advancement of breast cancer stem cells and genotyping and analyze the correlation between the two. Methods Relevant literatures about breast cancer stem cells and genotyping, which were published recently were collected and reviewed. Results Cancer stem cell origin theory was supported by researches of correlation between breast cancer stem cells and genotyping, which also explained the complexity of intrinsic subtypes and heterogeneity of breast cancer. Conclusions A new way can be detected to study the formation mechanism and biological characteristics of breast cancer at the cellular and molecular level by researches of correlation between breast cancer stem cells and genotyping, which are expected to provide new strategies and tools for diagnosis and treatment of breast cancer.