**1. Introduction**

Autoimmune diseases (ADs) can be classified as the inability of the human systems to distinguish their own bodies from foreign bodies [1, 2]. There have been more than 80 autoimmune diseases reported to date [3]. The immune system remains one of the most poorly understood systems in the human body. The COVID-19 pandemic has re-shed light on the immune system once again [4, 5]. ADs can be triggered in humans due to multiple factors such as environmental factors and genetic predisposition factors. The pathogenesis of the diseases can be hugely variable but the involvement of T and B lymphocytes from the adaptive immunity remains a hallmark for this umbrella of disease [6]. The increase in the detection and classification of ADs can be owed to

the development of serological tools to detect antibodies [7]. Autoimmune diseases can be classified as systematic and organ-specific diseases.

The Gastrointestinal Tract (GI tract) is a part of the digestive system in humans, and it is composed of six components: mouth, esophagus, stomach, small intestine, large intestine, and anus. The GI tract is prone to diseases, and it is affected by multiple factors in the pathogenesis of the disease and multiple manifestations of other systematic diseases appear in the GI tract. There are five common autoimmune diseases in the GI tract: (1) achalasia, (2) atrophic autoimmune gastritis (AAG), (3) celiac disease (CD), (4) eosinophilic esophagitis (EoE), and (5) inflammatory bowel diseases (IBD) which includes Crohn disease and ulcerative colitis (UC). The manifestation of other autoimmune diseases in the GI tract could be due to: (1) systematic mastocytosis, (2) systematic sclerosis and CREST syndrome, (3) autoimmune enteropathy, (4) autoimmune hepatitis, (5) autoimmune pancretitis, (6) mixed connective tissues disease, (7) primary sclerosing cholangitis and autoimmune sclerosing cholangitis, and (8) systemic lupus erythematosus (SLE). The review of the manifestation in the GI tract is beyond the scope of this chapter. This chapter covers the definition and etiology of autoimmune diseases, the relationship between autoinflammation and autoimmunity, an overview of the five diseases, the common antibodies that are used as a predictor factor for the disease, the role of gut-brain axis, and the psychological link in the GI tract autoimmune diseases, the role of nutrition in GI autoimmune diseases, and the treatment available for the diseases.
