Multiple sclerosis (MS) is an inflammatory demyelinating and neurodegenerative disorder of the central nervous system, which is associated with brain atrophy and volume changes in some brain structures. This study aimed to compare the volume of the basal ganglia, thalamus, cerebellum, and brainstem in patients with relapsing-remitting MS with that of the control group using magnetic resonance imaging (MRI). In this cross-sectional study, MRI brain scans were obtained from 25 patients with relapsing-remitting MS and 25 healthy control subjects. Volumetric analyses were performed using Brain Suite software. The mean age of the MS and the control groups was 33.96±8.75 and 40.40±8.72, respectively. No statistically significant difference was found in gender (P=0.747). The bilateral putamen and caudate nuclei volumes were significantly higher in the case group than in the control group (P<0.001). Moreover, lower the volume of the brainstem, cerebellum, bilateral thalamus, and globus pallidus were identified in the MS patients compared to the control group (P<0.001). There was an inverse correlation between the disease and treatment duration with the thalamus and cerebellum volume in MS patients (P=0.001). Treatment duration also had an inverse correlation with brainstem volume (P=0.047). The volume of some structures of the brain, including globus pallidus, thalamus, cerebellum, and brainstem is lower in MS and can be one of the markers of disease progression and disability among MS patients. Due to the degenerative process in multiple sclerosis, some cerebral structures may face volume change.The present study demonstrated that the volume of globus pallidus, thalamus, cerebellum, and brainstem is lower in MS patients compared to the controls. Multiple sclerosis (MS) is defined as an inflammatory disease involving the white matter of the brain, but experience has shown that many non-white matter structures also change in MS. In this study, we aimed to examine some parts of the brain, such as the thalamus, basal ganglia, brainstem, and cerebellum, for volume changes. The results showed that all these structures can have a smaller volume in MS patients than in healthy people. Especially in the case of the thalamus and cerebellum, this difference increases with increasing the disease duration. Changes in the size of these structures can be the result of degeneration of the neurons in these areas. These changes can cause significant disability in patients; however, there may not be significant changes in the number of plaques in patients. Attention to these changes can be essential in interpreting patients' clinical changes, including motor and cognitive disabilities.