Matrix metalloproteinases (MMPs) are a family of genes of the neutral proteinases that are important to normal development and to a variety of pathological processes including neuroinflammation. In the central nervous system (CNS), MMPs degrade components of the basal lamina, leading to disruption of the blood-brain barrier (BBB), and contribute to the neuroinflammatory responses. Their concentration in experimental allergic encephalomyelitis (EAE) increases a few folds and is accompanied by a thinner basal membrane in the early phase of EAE. After induction of oral tolerance by pretreatment with spinal cord hydrolisate proteins, the concentration of MMPs decreased by 30%. Other ultrastructural changes were observed in the early phase of EAE, i.e., karioskeletal damage with vesicular structures in karioplasm, compartmentalisation of the endoplasmic reticulum in perikarium, large cisterns of the Golgi apparatus, increased activity of microglial cells with numbers of phagolisosomes, disorganisation of sheets of myelin, neoangiogenesis in parenchyma of the cerebral cortex. After oral pretreatment with spinal cord hydrolisate proteins, no changes in karioskeletal proteins were found. Still Golgi apparatus spheres were large. Many pores in the nuclear membranes were observed, which is probably a sign of increased genetic information transport. We also observed some collagen fibrils as a sign of reparative processes. These results show the diminishing of inflammation in the early phase of EAE after oral induction of immunological tolerance and some possibilities of clinical implication in multiple sclerosis treatment.