Donor lymphocyte infusion (DLI) is typically used in 3 clinical situations: therapeutically for proven relapse of malignancy, prophylactically in patients with high-risk of relapse, and in case of mixed chimerism. Mixed chimerism, which occur after transplantation can be a sign of possible rejection. In case of increased mixed chimerism, immunotherapy with donor lymphocyte infusions could reverse this process. After DLI, both acute and chronic graft-versus-host disease and marrow aplasia are well-known toxicities. In this paper, we present a case report of young patient with chronic granulomatous disease (CGD) after allogeneic hematopoietic stem cell transplantation (allo-HSCT), with successful immunotherapy following mixed chimerism, which was complicated by bone marrow aplasia that required a second stem cell infusion. DLI seems to be an effective and highly promising treatment method of transplant rejection in patients with CGD but can induce bone marrow aplasia and may require a second stem cell infusion.