Introduction: Breast cancer is the commonest malignant tumour in females. Drug resistance and disease relapse are common problems occurring during treatment. Cancer Stem Cells (CSC) are implicated in tumourigenesis and resistance to therapy. Nanog is a transcription factor important for regulation of Embryonic Stem Cell (ESC) maintenance and survival. Whereas, Nestin, is a class VI intermediate filament protein that was primarily found during development in neural stem cells. They have been observed in CSC in several neoplasms. Aim: To evaluate the expression of Nanog and Nestin in breast carcinoma in Egyptian women and its relation to clinicopathologic parameters and prognosis. Materials and Methods: The current study was a prospective cohort study conducted in Zagazig University hospitals in Egypt in General surgery Department, Pathology Department and Clinical Oncology and Nuclear medicine Department during the period between September 2015 and September 2019. The study evaluated the immunohistochemical expression of Nanog and Nestin in 74 breast carcinoma cases. Results: The immunoexpression of Nanog and Nestin were related to high tumour grade, advanced TNM stage (TNM Classification of Malignant Tumors), nodal infiltration, lympho-vascular invasion, ER negative status, PR negative status and high Ki67 expression. Nestin expression was significantly associated with 4-year Disease Free Survival (DFS), and 4-year Overall Survival (OS) (p<0.001). Conclusion: Nanog and Nestin were poor prognostic markers of breast carcinoma patients and Nestin is superior to Nanog in predicting patients’ outcome.