The presence and number of circulating tumor cells (CTCs) in the blood of patients with solid tumors are predictive of their clinical outcomes. To date, the CellSearch system is the only US Food and Drug Administration‐approved CTC enumeration system for advanced breast, prostate, and colon cancers. However, sensitivity issues due to epithelial cellular adhesion molecule (EpCAM)‐based enrichment and limited capability for subsequent molecular analysis must be addressed before CTCs can be used as predictive markers in the clinical setting. We have developed a multicolor CTC detection system using cross‐contamination‐free flow cytometry, which permits the enumeration and characterization of CTCs for multiple molecular analyses. Tumor cell lines with different expression levels of EpCAM were spiked into peripheral blood obtained from healthy donors. Spike‐in samples were negatively enriched using anti‐CD45‐coated magnetic beads to remove white blood cells, and this was followed by fixation and labeling with CD45‐Alexa Fluor 700, EpCAM‐phycoerythrin, cytokeratin (CK)‐fluorescein isothiocyanate antibodies, and/or 7‐aminoactinomycin D for nuclei staining. Excellent detection (slope = 0.760–0.888) and a linear performance (R² = 0.994–0.998) were noted between the observed and expected numbers of tumor cells, independent of EpCAM expression. The detection rate was markedly higher than that obtained using the CellSearch system, suggesting the superior sensitivity of our system in detecting EpCAM− tumor cells. Additionally, the incorporation of an epithelial–mesenchymal transition (EMT) marker allowed us to detect EpCAM−/CK− cells and EMT‐induced tumor cells. Taken together, our multicolor CTC detection system may be highly efficient in detecting previously unrecognized populations of CTCs. © 2013 International Society for Advancement of Cytometry