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Autoimmune diseases are caused by the overactivity of the immune system towards self-constituents. Risk factors of autoimmune diseases are multiple and include genetic, epigenetic, environmental, and psychological. Autoimmune chronic inflammatory bowel diseases, including celiac and inflammatory diseases (Crohn's disease and ulcerative colitis), constitute a significant health problem worldwide. Besides the complexity of the symptoms of these diseases, their treatments have only been palliative. Numerous investigations showed that natural phytochemicals could be promising strategies to fight against these autoimmune diseases. In this respect, plant-derived natural compounds such as flavonoids, phenolic acids, and terpenoids exhibited significant effects against three autoimmune diseases affecting the intestine, particularly bowel diseases. This review focuses on the role of natural compounds obtained from medicinal plants in modulating inflammatory auto-immune diseases of the intestine. It covers the most recent literature related to the effect of these natural compounds in the treatment and prevention of auto-immune diseases of the intestine. [Display omitted] • Autoimmune chronic inflammatory bowel diseases constitute a health problem. • Crohn's disease and ulcerative colitis are examples of Autoimmune chronic inflammatory diseases • natural phytochemicals could be used to manage and treat autoimmune diseases • Flavonoids, terpenoids, and phenolic acids could be promising to treat autoimmune diseases. [ABSTRACT FROM AUTHOR]