A three-color flow cytometric method with a simultaneous negative and positive selection (SNAPS) approach has been developed to detect blood chimerism using a FITC-conjugated recipient-specific HLA monoclonal antibody, a biotinylated donor-specific HLA monoclonal antibody and Cy5-PE-conjugated streptavidin and a PE-conjugated CD3 monoclonal antibody. Detection of simulated blood chimerism at a frequency of 0.01% was achieved by SNAPS. In contrast, by one-color flow cytometry methods, chimerism can be detected at only about 3-4% with the same donor-specific HLA monoclonal antibody. The percentages of donor CD3 cells detected by SNAPS are proportional to the percentages of donor CD3 cells counted. SNAPS method provides a fast, sensitive and reliable way to analyze trace amounts of donor cells in a recipient's blood.