Stem cell homing has been studied in syngeneic models and appears to be rapid (<1 h) and dependent on cellular adhesion and migration factors. We utilized a full H2‐mismatched transplantation model to determine the basics of allogeneic homing. C57BL/6J Lin‐Sca‐1+ cells were labeled with CFSE and injected in non‐myeloablated BALB/c mice. Fluorescent cell detection was via high‐speed FACS analysis. Alternatively, B6.SJL whole bone marrow cells were injected in lethally irradiated BALB/c mice (10 Gy). One, 3, 6, and 24 h after transplant, marrow was harvested and cells were either plated for high proliferative potential colony‐forming cell (HPP‐CFC) assay or secondarily injected into myeloablated (8 Gy) C57BL/6J mice using 10% competing C57BL/6J marrow. Chimerism was evaluated at 8 weeks. CFSE+ cells were detected in the bone marrow 1, 3, and 6 h after injection. The numbers were moderately lower when compared to syngeneic homing possibly due to strain effect. Conversely, utilizing a surrogate or secondary assay, we observed a decline of secondary engraftment of harvested cells over time, but not of HPP‐CFC. Combining experiments and normalizing the 1‐h time point to 100% (to allow comparison), we observed a mean relative engraftment of 87 ± 29%, 72 ± 21%, 84 ± 35% of the 1 h level at 3, 6, and 24 h respectively. HPP‐CFC assay showed no significant variation as a homing surrogate over 1–6 h. These data indicate a rapid homing into allogeneic recipients with a plateau at 1 h. The decline of secondary engraftability over time may indicate a phenotype alteration of homed cells. J. Cell. Physiol. 211: 386–391, 2007. © 2006 Wiley‐Liss, Inc.