Objective. The aim of study: to investigate the functional changes in the thalamus, amygdala, and hippocampal region using functional MRI at rest and determine their clinical significance in various types of MS.Materials and methods. 68 patients with a diagnosis of multiple sclerosis (MS) were examined: 40 patients with a relapsing-remitting MS (RRMS) in remission and 28 patients with secondary progressive MS without signs of activity and progression (SPMS). The control group consisted of 10 healthy people of the appropriate age and gender without neurological and somatic diseases. All patients and controls underwent MRI of the brain on a Siemens Tim Trio tomograph with a magnetic field induction of 3.0 TL, using contrast enhancement, T1 gradient echo protocols, REST-BOLD, and subsequent processing of the data obtained using CONN 19с software.Results and conclusion. In the course of the study, various patterns of changes in functional connections were found: in patients with RRMS, there is a decrease in the intensity of connections of the thalamus with other brain structures and a decrease in their number. In patients with RRMS, a greater number and intensity of connections within the thalamus and other structures of the brain were detected compared to SPMS. In patients with RRMS, there is a significant decrease in the connectivity parameters of the hippocampal formation, which is expressed on the left, and in the case of the amygdala complex – on the right, this is manifested in a total decrease in the intensity of connections with other brain structures and a decrease in their number. Thus, the method of functional MRI at rest makes an additional contribution to the understanding of neurodegenerative processes in various phenotypes of multiple sclerosis.