Background. The purpose was to develop a prognosis assessment system based on clinical and mathematical analysis of indicators at different stages in various types of the course of multiple sclerosis. Materials and methods. Clinical (clinical neurological method and survey using a questionnaire developed at the Department of Autoimmune and Degenerative Pathology of the Nervous System of the State Institution “Institute of Neurology, Psychiatry and Narcology of the National Academy of Medical Sciences of Ukraine”) and mathematical and statistical (permutation test) methods were applied. Using the method of permutation (permutation test) in groups of patients with different types of multiple sclerosis, the differences in the mean values of clinical indicators were evaluated characterizing the type of multiple sclerosis course at different time stages: preclinical stage, the onset, recurrent stage for relapsing-remitting and secondary progressive multiple sclerosis, stage of progression — for secondary and primary progressive multiple sclerosis. On this basis, clinical indicators were identified, which with a high probability (confidence interval of 0.95) at each time stage of multiple sclerosis determine the final prognosis of the disease. Results. We have examined 280 patients: 80 (50 women and 30 men) with a relapsing-remitting course, 140 (80 women and 60 men) with a secondary progressive course and 60 (30 women and 30 men) with a primary progressive course of multiple sclerosis. The nature of prognosis (good and uncertain with a relapsing-remitting course, uncertain and poor with progressive types) was assessed on the basis of clinical and diagnostic criteria developed taking into account the features of the disease course as a whole. The studies have shown that a good prognosis is highly probable with a combination of clinical indicators such as mild onset, complete remission after onset, mild relapses developing rapidly, and long-term remission between relapses at a relapsing-remitting stage; uncertain prognosis — in the presence of moderate onset, stem symptoms at the onset, severe and moderate relapses, and a tendency to aggravate and lengthen relapses at a relapsing-remitting stage. A poor prognosis in a secondary progressive course is reliably associated with the chickenpox at the preclinical stage in a premorbid history, lightning-fast onset development, steady progression proceeding without clinically outlined periods of stabilization; uncertain prognosis — with a fast development of the onset. A poor prognosis in a primary progressive course was closely associated with severe traumatic brain injury at the preclinical stage in a premorbid history, cerebellar symptoms at the onset, formation of the progression stage immediately after the onset, without the stabilization period, steady type of progression at the stage of progression; uncertain prognosis — with herpetic infections at the preclinical stage in a premorbid history, mild onset, the formation of a progression stage after a stabilization period that occurred after the onset, incremental progression at the progression stage proceeding in the form of alternating periods of slow accumulation of neurological deficit, which, as a rule, has a local focus, and stages of stabilization with different duration. Conclusions. Thus, with the help of clinical and mathematical analysis, it was shown that the formation of alternative prognosis variants for different types of multiple sclerosis occurs through a selective involvement in a single pattern of clinical indicators that have diagnostic significance at different time stages of the course of the disease.