Primary immunodeficiencies (PID) include a group of congenital diseases, many of which are associated with a high risk of developing life-threatening infectious and non-infectious complications. Many of PIDs require hematopoietic stem cell transplantation (HSCT), which can lead to a complete cure of the disease. The article presents more than 20 years of experience in conducting HSCT with PID in the Russian Children's Clinical Hospital for the period from 1997 to 2018. 88 HSCTs were performed in 80 patients (64 boys and 16 girls) with various PIDs: severe combined immune deficiency (SCID, n = 34), hemophagocytic lymphohistiocytosis (HLH, n = 12), chronic granulomatous disease (CGD, n = 11), Wiskott–Aldrich syndrome (WAS, n = 10), congenital agranulocytosis (n = 4), hyper IgM syndrome type 1 (n = 3), Nijmegen breakage syndrome (n = 2), lymphoproliferative syndrome (n = 2), Chediak–Higashi syndrome (n = 1), leukocyte adhesion deficiency (n = 1). Оverall survival (OS) and event-free survival (EFS) after HSCT with PID was 63.1% and 49.3%. OS after HSCT with SCID was 65.5%, EFS – 48.4%. The article presents the results of HSCT taking into account the type of HSCT, the source of hematopoietic stem cells (HSC) and the type of graft manipulation, conditioning regimen. Growth of positive results of HSCT in patients with PID in recent years is associated with the improvement of accompanying therapy (improving the quality of infection control, the introduction of new drugs for the prevention and treatment of hepatic veno-occlusive disease); technology application TcRα+β+/CD19+ depletion at haploidentical transplantation; optimization of conditioning regimens; successes in the prevention and treatment of the graftversus- host disease (antithymocyte globulin and rituximab administration during the period of conditioning, post-transplant administration of cyclophosphamide at haploidentical HSCT). The study was approved by the Independent Ethics Committee of Russian Children's Clinical Hospital.