A majority of breast cancers are estrogen receptor (ER) positive and have a luminal epithelial phenotype. However, these ER⁺ tumors often contain heterogeneous subpopulations of ER⁻ tumor cells. We previously identified a population of cytokeratin 5 (CK5) positive cells within ER⁺ and progesterone receptor positive (PR⁺) tumors that is both ER⁻PR⁻ and CD44⁺, a marker of breast tumor-initiating cells (TICs). These CK5⁺ cells have properties of TICs in luminal tumor xenografts, and we speculated that they are more resistant to chemo- and anti-ER-targeted therapies than their ER⁺ neighbors. To test this, we used ER⁺PR⁺ T47D and MCF7 breast cancer cells. CK5⁺ cells had lower proliferative indices than CK5⁻ cells, were less sensitive to 5-fluorouracil and docetaxel, and cultures became enriched for CK5⁺ cells after treatments. CK5⁺ cells were less prone to drug-induced apoptosis than CK5⁻ cells. In cells treated with 17β-estradiol (E) plus anti-estrogens tamoxifen or fulvestrant, ER protein levels decreased, and CK5 protein levels increased, compared to controls treated with E alone. In ER⁺ tumors from patients treated with neoadjuvant endocrine therapies ER gene expression decreased, and CK5 gene expression increased in post compared to pre-treatment tumors. The number of CK5⁺ cells in tumors also increased in post- compared to pre-treatment tumors. We conclude that an ER⁻PR⁻CK5⁺ subpopulation found in many luminal tumors is resistant to standard endocrine and chemotherapies, relative to the majority ER⁺PR⁺CK5⁻ cells. Compounds that effectively target these cells are needed to improve outcome in luminal breast cancers.