**Abstract**

Autoimmune diseases have emerged as a pandemic in our modern societies, especially after World War II. There are currently more than 80 autoimmune diseases that compromise the lives of millions of patients around the world. There is a variety of factors that are involved in the pathogenesis of autoimmune diseases that vary from environmental factors to genetic susceptibility. The GI tract is one of the most susceptible sub-systems in human bodies for autoimmune organ-specific diseases. There are five autoimmune GI tract diseases that are most common. This review consists of two chapters. In part I, we shed the light on introducing the concept of autoimmunity, the description of the disease's pathogenesis and the diagnosis, the link between the gut and brain through what is known as the gut-brain axis, and the relationship of this axis in GI autoimmune diseases. In part II, we will shed light on the role of antibodies as markers for the prediction of the disease, artificial intelligence in GI autoimmune diseases, the nutritional role and implications in the five GI autoimmune diseases, and finally the treatment of those diseases.

**Keywords:** achalasia, atrophic autoimmune gastritis, celiac disease, eosinophilic esophagitis, inflammatory bowel diseases, Crohn disease, ulcerative colitis, immunological continuum, epithelial barrier dysfunction, gut-brain axis
