BACKGROUND: Multiple sclerosis is a chronic autoimmune disease characterized by multifocal foci of demyelination in the central nervous system, usually affecting people of working age. The disease causes damage to the blood-brain barrier, the development of multifocal inflammation, destruction of the myelin sheath of axons and various degrees of damage. It is clinically manifested by restriction of motor activity, visual acuity, as well as other symptoms leading to loss of performance and disability of the patient. AIM: determination of changes in the functional connectivity of brain neural networks in patients with multiple sclerosis before and after high-dose immunosuppressive therapy and autologous hematopoietic stem cell transplantation by performing functional magnetic resonance imaging at rest. MATERIALS AND METHODS: The data of functional magnetic resonance imaging of patients with multiple sclerosis were analyzed in dynamics before and after the use of high-dose immunosuppressive therapy followed by autologous hematopoietic stem cell transplantation. The study involved 25 patients with a verified diagnosis of multiple sclerosis. Each underwent complex magnetic resonance imaging at two time points (before and after high-dose immunosuppressive therapy followed by autologous hematopoietic stem cell transplantation) with a difference of 12 months, which included structural magnetic resonance imaging - in order to exclude the presence of pathological foci in the brain (in addition to foci of multiple sclerosis) and functional magnetic resonance imaging.-resonance imaging at rest — to assess functional connectivity. Also, according to the method generally accepted in classical neurology, a clinical neurological examination was performed. RESULTS: At the stage of comparing data on the two groups obtained using functional magnetic resonance imaging at rest, changes in functional activity were detected in various parts of the brain, presumably responsible for clinical differences in the studied groups. CONCLUSION: Currently, the links between brain structures and morphological changes that cause cognitive impairment in multiple sclerosis are being studied. To predict the progression of the disease, the development of biomarkers, including those based on functional magnetic resonance imaging, is required. Evaluating changes in the functional connectivity of brain neural networks can help personalize therapeutic and rehabilitation approaches.