Delayed immune reconstitution remains a major cause of morbidity associated with myelosuppression induced by cytotoxic therapy or myeloablative conditioning for stem cell transplant, as well as potentially lethal doses of total- or partial-body irradiation. Restoration of a functional immune cell repertoire requires hematopoietic stem cell reconstitution for all immune cells and effective thymopoiesis for T cell recovery. There are no medical countermeasures available to mitigate damage consequent to high-dose, potentially lethal irradiation, and there are no well characterized large animal models of prolonged immunosuppression to assess efficacy of potential countermeasures. Herein, the authors describe a model of T and B cell reconstitution following lethal doses of partial-body irradiation with 5% bone marrow sparing that includes full exposure of the thymus. Rhesus macaques (n = 31 male, 5.5-11.3 kg body weight) were exposed to midline tissue doses of 9.0-12.0 Gy using 6 MV LINAC-derived photons at a dose rate of 0.80 Gy min, sparing approximately 5% of bone marrow (tibiae, ankles, and feet). All animals received medical management and were monitored for myeloid and lymphoid suppression and recovery through 180 d post-exposure. Myeloid recovery was assessed by neutrophil and platelet-related hematological parameters. Reconstitution of B and T cell subsets was assessed by flow cytometric immunophenotyping, and recent thymic emigrants were identified by RT-PCR of T cell receptor excision circles. Mortality was recorded through 180 d post-exposure. Acute myelo-suppression was characterized by severe neutropenia and thrombocytopenia, followed by recovery 30-60 d post-exposure. Total T (CD3+) and B (CD20+) cells were reduced significantly following exposure and exhibited differential recovery patterns post-exposure. Both CD4+ and CD8+ subsets of naïve T cells and total CD4+ T cell counts remained significantly lower than baseline through 180 d post-exposure. The failure of recent thymic emigrants and naïve T cell subsets to recover to normal baseline values reflects the severe radiation effects on the recovery of marrow-derived stem and early thymic progenitor cells, their mobilization and seeding of receptive thymic niches, and slow endogenous thymic regeneration.