Immunodeficient NOD.Cg-Prkdcscid Il2rgtm1Wjl/ SzJ (NSG) mice are a valuable resource to study human hematopoietic stem cells. Prolonged multilineage hematopoiesis indicates stem cell engraftment and generally is measured by flow cytometry. In this study, we took advantage of the multi-parameter detection afforded by modern flow cytometers to optimize detection of human hematopoiesis in NSG mice. Antigens widely expressed by mouse or human cells were evaluated as markers to distinguish mixtures of these cells to optimize and test the limits of chimerism detection. The bone marrow, spleen, and liver of NSG mice transplanted with human hematopoietic cells were analyzed for evidence of engraftment. Mouse bone marrow cells were best marked for exclusion by staining with a combination of CD45, TER-119, and anti-H-2Kd monoclonal antibodies, whereas live human cells were most accurately identified by elimination of cell doublets and positive staining for CD59. Human stem cells (CD34++CD133+CD38low) and progenitors were detected in the bone marrow and liver, but not in the spleen. An unusual pattern of myeloid antigen expression was detected in the bone marrow and CD3+CD4+CD8+ T-cells were detected in the spleen. We concluded that multicolor flow cytometric analysis that clearly distinguishes mouse and human cells offers accurate detection of human chimerism in NSG mice. Human hematopoiesis can be detected in the bone marrow and liver of NSG mice with T-lymphopoiesis, possibly occurring in the spleen.