Key Points• T SCM are abundant early after allogeneic hematopoietic stem cell transplantation and derive from naive T cells that survived pt-Cy.• Pt-Cy allows the generation of donor primary and recall responses in transplanted patients, even in the presence of persistent antigen.Early T-cell reconstitution following allogeneic transplantation depends on the persistence and function of T cells that are adoptively transferred with the graft. Posttransplant cyclophosphamide (pt-Cy) effectively prevents alloreactive responses from unmanipulated grafts, but its effect on subsequent immune reconstitution remains undetermined.Here, we show that T memory stem cells (T SCM ), which demonstrated superior reconstitution capacity in preclinical models, are the most abundant circulating T-cell population in the early days following haploidentical transplantation combined with pt-Cy and precede the expansion of effector cells. Transferred naive, but not T SCM or conventional memory cells preferentially survive cyclophosphamide, thus suggesting that posttransplant T SCM originate from naive precursors. Moreover, donor naive T cells specific for exogenous and self/tumor antigens persist in the host and contribute to peripheral reconstitution by differentiating into effectors. Similarly, pathogen-specific memory T cells generate detectable recall responses, but only in the presence of the cognate antigen. We thus define the cellular basis of T-cell reconstitution following pt-Cy at the antigen-specific level and propose to explore naive-derived T SCM in the clinical setting to overcome immunodeficiency. These trials were registered at www.clinicaltrials.gov as #NCT02049424 and #NCT02049580. (Blood. 2015;125(18):2855-2864