Regeneration of the bone marrow microenvironment after transplantation of allogeneic hematopoietic stem cells is poorly explored. The goal of our study was to investigate this process focusing on immunologic factors: concentrations of selected cytokines, expression of immunosuppressive proteins CD47 and CD274 on hematopoietic stem cells, and frequency of T regulatory lymphocytes (Tregs). Bone marrow samples were collected before transplantation, on the day of transplantation, and at the 1-year follow-up. As a control group, we used bone marrow from healthy donors. Prior to the conditioning, the percentage of Tregs and concentration of interleukin-10 were higher in the bone marrow of patients than in healthy donors. The conditioning regimen resulted in increased concentrations of interferon-γ and expression of CD274 on hematopoietic stem cells. Twenty-eight days after transplantation, level of Tregs, expression of CD47, and concentration of interleukin-10 and latency-associated peptide 1 were increased compared with the period before conditioning. Starting from day 100 after transplantation, the microenvironment tended to normalize; the level of Tregs and concentrations of most cytokines were similar to values in the bone marrow of healthy donors.