Background In metastatic breast cancer (MBC) the molecular characterization of Circulating Tumor Cells (CTCs) provides a unique tool to understand metastasis-biology and therapy-resistance. We evaluated the prognostic significance of gene expression in EpCAM(+) CTCs in 46 MBC patients based on a long follow-up. Methods We selected a panel consisting of stem cell markers (CD24, CD44, ALDH1), the mesenchymal marker TWIST1, receptors (ESR1, PGR, HER2, EGFR) and the epithelial marker CK-19. Singleplex RT-qPCR was used for TWIST1 and CK-19 and multiplex RT-qPCR for a) CD24, CD44, ALDH1, HPRT and b) ESR1, PR, HER2, EGFR. A group of 19 healthy donors (HD) was used as control. Results Univariate (p=0.001) and multivariate analysis (p=0.002) revealed the prognostic value of combined gene expression of CK-19(+), CD44high/CD24-/low, ALDH1high/CD24-/low and HER2 over-expression for overall survival (OS). The Kaplan–Meier estimates of OS were significantly different in patients positive for CK-19 (p = 0.028), CD44high/CD24-/low (p = 0.002), ALDH1high/CD24-/low (p = 0.007) and HER2-positive (p = 0.022). Conclusions Our results indicate that combined gene expression analysis in EpCAM(+) CTCs provides prognostic information in MBC but need to be further confirmed in a prospective study, including a larger and well-defined patient cohort.