A continuous flow, magnetic separation method has been proposed to isolate large numbers of cells for clinical and biotechnological applications. The separation system, based on the quadrupole magnet flow sorter, has been tested on magnetically labeled, human blood progenitor cells using monoclonal antibody against the cluster of differentiation 34 (CD34) molecule and a magnetic colloid. A small volume of the cell suspension was injected into the sorter at variable volumetric flow rates, and the resulting cell elution profiles were analyzed for cell recovery in the magnetically enriched and depleted cell fractions. Independently, the cell motion in the magnetic field has been analyzed using a novel technique of cell tracking velocimetry, which allowed the determination of cell magnetophoretic mobility. A mathematical model of the cell motion inside the quadrupole flow sorter was used to calculate the recovery of the sorted fractions based on the cell magnetophoretic mobility distribution. A comparison of experimental and theoretical data allowed the verification of assumptions underlying the magnetic cell separation process, and provided guidelines for engineering design of the magnetic flow sorter.