High-dose immunosuppressive therapy with autologous hematopoietic stem cell transplantation (HDIT-AHSCT) is a promising and effective method of treatment of autoimmune diseases, including multiple sclerosis. Over the past 20 years, the frequency and severity of side effects of therapy have been significantly reduced due to the accumulation of experience of transplant centers, changing principles of patient selection and decreased intensity of conditioning regimens. However, the medium-intensity therapeutic protocols may also be accompanied by complications. We have analyzed the literature data and our own experience on early and late side effects of HDIT-AHSCT. The profile of an appropriate schedule of HDIT-AHSCT is also presented, as determined by characteristics of the patients and the clinical course of multiple sclerosis. The types of HDIT-AHSCT are formulated, as based on the goals and expectations of the treatment approach.