Over the past twenty-five years, there has been a significant effort focused on the use of cellular grafts with low or no potential to develop Graft-versus-Host Disease (GvHD) to treat patients after myeloablative procedures. T-cells, which typically express CD3 antigen and are thought to be responsible for GvHD, have been identified as the general target cell population to deplete from an allogeneic cell graft. Immunomagnetic cell separation is one of the most promising techniques in the separation and depletion of T-cells due to its high efficiency and speed. A key element of immunomagnetic techniques is the characteristics of the immunomagnetic labels. In this study, the authors described the preparation and characterization of a new CD3-Superparamagnetic Carboxyl Beads. The anti-CD3 antibody labeling density was determined by BCA method. Jurkat cells expressing the same antigen with T-cells were used as the target cells to test the effectiveness of immunomagnetic labeling process. The magnetophoretic mobilities of labeling samples were measured by our previously developed, and reported, Cell Tracking Velocimetry instrument. A novel flow-through immunomagnetic cell sorting system (Quadrupole Magnetic Cell Sorter, QMS) was used to perform the depletion of magnetic labeling Jurkat cells, which has been developed in the author's laboratories. Under optimized conditions, the yield of CD3- cells was 90%, and the log depletion of CD3+ cells was 3.2 at the cell-sorting rate of 1×106 cells/s.