CD45.1/CD45.2 congenic markers have been frequently used to track hematopoietic lineage differentiation following hematopoietic stem and progenitor cell (HPSC) transplantation. However, several studies suggest that a bias exists in CD45.1 versus CD45.2 hematopoietic cell reconstitution from the transplanted HPSCs. Meanwhile, no definitive comparison has been reported for mature immune cells as to whether the CD45.1/CD45.2 disparity can skew immune cell response. In this study using lymphocytopenia Rag1-/- CD45.2 mice as hosts, we assessed the proliferative potential of CD45.1 versus CD45.2 lymphocytes following adoptive transfer of mature T and B cells harvested from the spleens of CD45.1 and CD45.2 mice. We have found that a selective bias for CD8+ T cells in that CD45.1 CD8+ T cells showed significantly higher proliferation and higher expression of PD-1 compared CD45.2 CD8+ T cells in the Rag1-/- CD45.2 hosts. This bias is likely due to MHC-I restricted allogeneic stimulation as CD45.1 versus CD45.2 CD4+ T cells and CD19+ B cells contained the same graft as CD8+ T cells showed equivalent proliferation. These results suggest that CD45.1/CD45.2 markers induce an alloreactive response specific to CD8+ T cells, and therefore call for caution for using them.