Autophagy is an integral part of cell strategy to overcome adverse living conditions. Moreover, autophagy participates in the protection of cytoplasm against invasion of the intracellular pathogenic bacteria. Abnormalities in the autophagy are participating on the inability of Crohn's disease patients to maintain gut microbiome homeostasis ultimating in the development of immunopathological reaction in these patients. Autophagy can enhance the survival of autoreactive T cells in multiple sclerosis patients thus contributing to the disease induction and progression.