Abstract We are employing a “liquid biopsy” approach for monitoring drug responses to new anti-cancer agents in early stage clinical trials by measuring drug effects in circulating tumor cells (CTCs), which requires the capability to capture and characterize CTCs from patients with diverse diseases including sarcomas, lymphomas and carcinomas. We have been applying the Apostream platform (DEP-FFF separation) with fluorescence imaging and have recently added the 5-channel CellSearch system (MAb coated ferrofluid) for specimen analysis. Use of both CD146 and EpCam capture per specimen, with addition of vimentin and the tumor markers, significantly increased the number of CTCs captured with the 5 channel CellSearch®. A “homebrew” CTC kit was developed that captures circulating cells that are either EpCAM or CD146 marker positive, and it was capable of identifying high numbers of EMT+ tumor marker+ double positive cells in patient specimens. There was statistical equivalency of events flagged as CTCs (CD45-/EpCam+/CK+) in patient specimens analyzed using Apostream or 5-Color CellSearch versus 4-channel CellSearch and 100% concordance between the CellSearch platforms. Reproducibility, as assessed by image re-analysis using Definiens software, was also high (>90%). Tumor marker specificity was established by analyzing normal donor blood, which varied from zero to 2 cells per ml blood depending on the marker set employed (only CD45 negative cells assessed). This approach solves a major limitation of using CTCs to monitor pharmacodynamic response by enumerating statistically significant cell numbers from patients with solid tumors of diverse histologies. Strikingly, both platforms demonstrated the presence of high numbers of CTCs with the Epithelial-Mesenchymal Transition (EMT) phenotype (10-100 cells per ml in Phase 1 trial populations), and widely used tumor markers such as MUC1, CEA, TLE1, or proteins generated by recombination events such as ASPL-TFE3. The presence of large numbers of CTCs expressing the EMT phenotype may be related to the intensive prior treatment (>3 prior therapies, median) of our phase 1 population. Funded by NCI contract # HHSN261200800001E. Citation Format: Lihua Wang, Francis Owusu, Sonny Khin, Ralph Parchment, Alice Chen, Shivaani Kummar, James H. Doroshow, Robert J. Kinders. Characterization and Enumeration of Multiple Circulating Tumor Cell Phenotypes Using Two Distinct Platforms Establishes Presence of Epithelial-Mesenchymal Transition CTCs in Patients. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr LB-B20.