Background: Breast cancer is one of the most common cancers with a high mortality rate worldwide including Saudi Arabia. It is characterized by the presence of both intra-and inter-tumor heterogeneity. It describes the origin of this heterogeneity to the cancer stem cells (CSC). Breast cancer stem cells are characterized by the expression of the surface markers CD44 and lack or very low expression of CD24. Objectives: To assess cancer stem cell markers (CD44 andCD24) in 126 breast cancer cases by immunohistochemistry and study their association with a different type of TP53 gene mutations by applying next-generation sequencing (NGS). In addition to analyze the association between these markers and the clinicopathological characteristics. Results: CD44 expression was significantly associated with lymph node metastasis, tumor grade, stage (each P<0.0001), and ER expression (P = 0.016). CD24 expression was found to be associated with lymph node metastasis and ER only. For the molecular analysis, the number of mutations per case was significantly associated with the advanced stage of breast cancer (p = 0.004). Also, missense mutation was highly associated with CD44 and CD24 (p=0.04, p=0.005), respectively. Stop-gained mutation and Frameshift mutation both were associated with CD44 only (p=0.01, p=0.05), respectively. Finally, the synonymous mutation was only associated with the stage of cancer (p=0.01). Conclusion, we believe that the combination of CD44, CD24, TP53 and TP53 gene mutations can be prognostic factors for breast cancer patients and the information obtained may contribute to the development of a treatment.