The diagnosis of diseases of the brain is based on additional methods, confirming the clinical diagnosis. One of the most objective methods is magnetic resonance imaging (MRI). A detailed quantitative evaluation became possible after the introduction of MRI voxel‐morphometry–statistical analysis of structural MRI images using a computerized segmentation matter of the brain gray and white matter. The decrease in the volume of the brain, as a manifestation of cerebral atrophy, is a common feature of many neurological diseases. We performed a study of brain structures in multiple sclerosis, Parkinson’s disease, and cerebrovascular diseases. In patients with multiple sclerosis the correlation was found between the score on a scale of Expanded Disability Status Scale and the total thickness of the cerebral cortex. In our study of the brain in Parkinson’s disease, the amount of the substantia nigra was slightly lower than in the control. In patients with long‐following Parkinson’s disease, the volume of substantia nigra was significantly higher than in patients with early stage. The increased volume was determined by the accumulation of organic iron compounds as a sign of neurodegeneration.