Purpose: We aimed to generate a capture platform that integrates a deterministic lateral displacement (DLD) microfluidic structure with magnetic-activated cell sorting (MACS) technology for miniaturized, efficient, tumor antigen-independent circulating tumor cell (CTC) separation. Methods: The microfluidic structure was based on the theory of DLD and was designed to remove most red blood cells and platelets. Whole Blood CD45 MicroBeads and a MACS separator were then used to remove bead-labeled white blood cells. We established HepG2 human liver cancer cells overexpressing green fluorescent protein by lentiviral transfection to simulate CTCs in blood, and these cells were then used to determine the CTC isolation efficiency of the device. The performance and clinical value of our platform were evaluated by comparison with the Abnova CytoQuest (TM) CR system in the separating of blood samples from 12 hepatocellular carcinoma patients undergoing liver transplantation in a clinical follow-up experiment. The isolated cells were stained and analyzed by confocal laser scanning microscopy. Results: Using our integrated platform at the optimal flow rates for the specimen (60 mu l/min) and buffer (100 mu l/min per chip), we achieved an CTC yield of 85.1% +/- 3.2%. In our follow-up of metastatic patients, CTCs that underwent epithelial-mesenchymal transition were found. These CTCs were missed by the CytoQuest (TM) CR bulk sorting approach, whereas our platform displayed increased sensitivity to EpCAM(low) CTCs. Conclusions: Our platform, which integrates microfluidic and MACS technology, is an attractive method for high-efficiency CTC isolation regardless of surface epitopes.