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Embryonic Stem (ES) cells are cell lines derived directly from the pre-implantation embryo. The generation of pure populations of neural progenitors from ES cells and their further differentiation into neurons, astrocytes and oligodendrocytes allows the potential use of these cells for the cure of neurodegenerative diseases and for neural drugs testing. An integrated device based on magnetophoresis, including microfluidic channels and incorporated high magnetic field gradients, was used to control the motion of cells, labeled with magnetic particles (MPs), through a biochip. This will result in a device capable of high-throughput separation at low cost. The separator was fabricated in polydimethylsiloxane (PDMS) comprising an inlet channel for cells 200 μm wide and inlet channel for buffer solution 700 μm wide. This device allows high separation efficiency of MP’s even when using inlet laminar fluid velocities up to 30 mm/s, by using a 15 mm wide and 60 μm thick separation chamber. The permanent magnet used was the W-12-Nfrom Supermagnete® made from an alloy of neodymium, iron and boron (Nd2Fe14B).In this work, the magnetophoretic device has been used for depletion of tumorogenic pluripotent stem cells from 46C mouse ES cell cultures by the specific recognition and labeling of the stage specific embryonic antigen 1 (SSEA-1). Purity degrees ranging from 95% to 99% were obtained and determined by flow cytometry analysis. These results raise the possibility of using this micro-device for the purification of human neural progenitor cultures from tumurogenic pluripotent stem cells.