Aldehyde dehydrogenase 1 (ALDH1) is a breast cancer stem cell (BCSC) marker related to clinical outcomes in breast cancer and have been proposed to chemo-resistance. The aim of this study was to analyze the breast cancer stem cells identified by ALDH1 and their association with clinico-pathological characteristics and outcomes after NAC. Patients and Methods: This is a prospective study conducted at medical oncology out-patient clinics of the National Cancer Institute, Cairo University (The NCI's, Tagamoa Al Awal branch) between January 2018 and June 2018. Women with locally advanced breast cancer were assigned to receive four cycles of anthracycline-based chemotherapy, followed by four cycles of taxane therapy with or without tarstuzumab. Tumor specimens were collected at baseline, and then at surgical resection. Cancer Stem Cells were determined by positive expression of ALDH1 by immunophentyping and correlated with pathological response after NAC, rate of breast conserving surgery, and disease free survival. Results: Eighty-one female patients were enrolled between January 2018 and June 2018. Mean age of the patients at time of diagnosis was 45.8 ± 9.1 years. Main pathologic subtype was duct carcinoma. Median follow up was 39.2 months. There was a positive association between BCSCs identified by ALDH1 expression and pathological response (p value = .026), and BCS (p value = .037). Also there was association between ALDH1 expression and ER negativity (p value = .016). No significant association between ALDH1 and DFS (p value = 0.839). HTIL were associated with ER negativity (p value = .006), high tumor proliferation marker ki67 (p value = .009), and pCR (p value = .001). Conclusions: The results of this study may indicate a role for BCSCs identified by ALDH1 expression in chemo-responsiveness, rather than chemo-resistance, after NAC in breast cancer patients. Further research remains necessary to confirm this result