Cancer stem cell-like cells (CSCs) are cancer cells that have the ability of self-renewal and differentiation into multiple malignant cell types (hierarchy). Thus, can cause relapses and metastasis. CSCs’ phenotype is defined by special transcription factors such as Nanog, Oct3/4, Sox2, Nestin, and CD34. The present study aims to determine the change in gene expression of the above markers in correlation with the stage of the disease in breast cancer patients. Initially, whole blood samples from patients with breast cancer were collected, followed by the isolation and culture of circulating tumor cells (CTCs). This was followed by the quantification of CSCs from the above cultures. CSCs’ molecular analysis was performed with qPCR, with the use of gene specific primers. At the same time of the analysis, the clinical assessments of the patients were requested from their physicians. The results indicated a linear relationship between the gene expression of stemness markers and the stage of the disease, as well as specific expression patterns by stage. It seems that these genes have an important role in the progression of the disease, thus they might be target for new treatment approaches.