We report a microchip system based on a combination of immunomagnetic separation and microfluidics for high-throughput detection of whole cells. In this system target cells bound to magnetic beads flow parallel to a microchip with flow rates of mLs/min. A magnetic field draws the bead-bound cells toward the microchip which contains apertures that allow passage of unbound beads while trapping the target cells. The cells can be analyzed clearly under a microscope and released from the chip for further analysis by removing the magnetic field. The system was characterized by detecting breast cancer cells (MCF-7) and lung cancer cells (A549) in culture media using anti-EpCAM conjugated magnetic beads. We were able to detect MCF-7 cells with > 90% yield using a flow rate of about 4 mL/min, and A549 cells with 78% yield with 1 mL/min. We also demonstrated high-throughput detection of cells with concentrations as low as 0.8 cells/mL in large sample volumes (12 mL). We expect this system to be useful in a wide variety of settings including detection of rare cells for clinical applications.