Isolation of primitive blood stem cells by different methods results in cell populations with distinct biological activities. This study was aimed at resolving differences in the frequency of multilineage reconstituting cells (MRC) and their precursors (pMRC) in cell populations isolated by positive selection for Sca-1 compared to those isolated by negative selection for 15-1.1. Separation of wheat germ agglutinin-positive mouse bone marrow cells into 15-1.1neg or Sca-1+ subsets was performed by flow cytometry. The isolated cells were transplanted into W/Wv or normal irradiated recipient mice and reconstitution was evaluated over time. Sca-1 + cells were less frequent and contained more MRC than 15-1.1 neg cells, while pMRC were found mainly among 15-1.1neg cells. MRC activity was exclusively contained within the Sca-1+ subpopulation of 15-1.1neg cells, but marrow from 7 robustly engrafted W/Wv mice did not contain donor-derived MRC, indicating that 15-1.1negSca-1+ cells contain low numbers of pMRC. Functional differences between 15-1.1neg and Sca-1+ cells were further confirmed by reverse transcriptase (RT)-PCR gene expression analysis. Early hematopoiesis-specific transcription factors (Scl, Gata-2, and Gata-1) were amplified from cDNA prepared from Sca-1+ but not 15-1.1neg cells. This study indicates that cell populations isolated as Sca-1+ are functionally distinct from those isolated as 15-1.1neg in that few pMRC are included among Sca-1+ cells and that MRC and pMRC are two distinct and separable cell populations.