Liquid biopsy is the new era in cancer diagnosis. Circulating Tumor Cells (CTCs) can provide useful information regarding prognosis and disease monitoring during treatment. In the last two decades CTCs’ enumeration and phenotypic characterization have demonstrated encouraging results regarding useful biomarkers for potential future targeted therapies. There are also studies showing that patients treated based on their CTC phenotype rather than their primary tumor had a better outcome, suggesting a critical role of these cells for breast cancer patients. However, they have not be integrated yet in common clinical practice due to their low abundance. Furthermore, their detection is mostly based on epithelial markers such as EpCAM and Cytokeratin, however it has been reported that CTCs, may express low levels of epithelial antigens. One possible mechanism responsible for the loss of epithelial markers in CTCs is epithelial-to-mesenchymal transition (EMT). This EMT phenotype make them invisible in the bloodstream. We have recently shown that some populations of CTCs may express EMT stem cell markers. We have also identified new biomarkers with clinical relevance for the patients, such as JUNB, CXCR4, PD-L1, HER2, Microtentacles, Detyrosinated Tubulin (GLU) etc.  In addition, we have developed new culture methods for these cells to test new drugs that can effectively target CTCs to eliminate the spread of cancer.