The choice of the optimal donor in the absence of an HLA-compatible relative, as well as the analysis of the risks of hematopoietic stem cell transplantation (HSCT), is extremely important, especially in patients with non-cancerous diseases. The article analyzes 99 allogeneic HSCTs from unrelated donors in the bone marrow transplantation department of the Russian Children’s Clinical Hospital. The analysis included patients with acquired and congenital forms of non-malignant diseases. The choice of an optimal unrelated donor in the absence of a compatible relative donor, as well as an analysis of the risks of treatment, requires studying the factors that influence the outcome of treatment in this group of patients. It was shown that the level of 2-year overall survival (OS) was 74 % (standard deviation ± 4.7 %). At the same time, clinical manifestations of the acute graft versus host disease of grade I–IV were recorded in 67 % (n = 66) of patients, and severe forms of grade III–IV in 13 % (n = 13) of children. Chronic graft versus host disease (chGVHD) was observed in 29 % (n = 29) patients. When studying the factors associated with the donor, it was found that the differences in the HLA system have a negative effect on the incidence of chGVHD; in a (9/10) HLA-incompatible donor, it was 29 % higher (p = 0.019). Increasing the age of the donor for every 10 years consistently reduces the OS by 9–11 % (p = 0.117), however, the OS with a donor over 46 years old was 100 % (n = 7). No effect on the agents with respect to the following factors with respect to the recipient was found: by sex, blood group, serostatus for cytomegalovirus (CMV). It was noted that the combination of CMV-positive serostatus of the donor and the negative status of the recipient increases the risk of transplant rejection up to 50 % in comparison with other variants of CMV serostatus (p = 0.001). In general, the possibility of performing HSCT from an unrelated donor for patients with non-malignant diseases and possible ways of selecting the optimal donor was noted. Conflict of interest. The authors declare no conflict of interest.Funding. The study was performed without external funding.