Background Tumor cells with a mesenchymal phenotype and/or cancer stem-like cells (CSCs) are known to contribute to metastasis and drug resistance. Circulating tumor cells (CTCs) undergoing epithelial-mesenchymal transition (EMT) and CTCs reflecting a dedifferentiated CSC phenotype may not be detected using only an anti-EpCAM antibody to capture them. We used an antibody-independent CTC enrichment platform, ApoStream ® , which does not rely on any antibody, including anti-EpCAM, to capture EMT-and CSC-CTCs in breast cancer patients who received neoadjuvant chemotherapy and correlated them to pathological complete response (pCR). Methods Blood samples from newly diagnosed breast cancer patients were prospectively collected before neoadjuvant chemotherapy (T 0), after chemotherapy but before surgery (T 1), and after surgery (T 2) and processed using ApoStream. CTCs detected were stained with additional markers to define 3 CTC subsets with the following phenotypes: epithelial CTCs (CK +, EpCAM+ or E-cadherin+), EMT-CTCs (β-catenin+ or vimentin+), and CSC-CTCs (CD44 + and CD24 low). Results We enrolled 55 patients, 47 of which had data for analysis.