Autoimmune connective tissue diseases (ACTDs) are heterogeneous disorders associated with different manifestations, clinical course of disease and prognosis among patients. Although recent advances in understanding the pathogenesis have led to major progress in target-oriented therapy, they still remain incurable. Novel biological drugs, cellular therapy and hematopoietic stem cell transplantation (HSCT) are real hopes for treatment development in the future. The concept of both autologous and allogeneic HSCT in children with autoimmune diseases is developing energetically since 1996, when the first HSCT was performed. Nowadays, after 17 years of clinical experience, both types of HSCT remain attractive and powerful salvage methods of treatment. However, there are still many doubts and unclear issues, which need further investigation. In the present review, we provide an overview of the knowledge concerning actual data on HSCT in a pediatric group of patients with different ACTDs, focused on juvenile idiopathic arthritis, systemic lupus erythematosus and systemic sclerosis.