In pediatric gastroenterology and hepatology, autoimmune diseases, such as inflammatory bowel diseases, celiac disease, and autoimmune hepatitis, are challenging for practitioners due to their increasing incidence, high morbidity, and substantial impact on children's quality of life. These conditions share similar pathophysiological mechanisms, including genetic predisposition, the role of the microbiome, and the influence of environmental and immunological factors. This review aims to explore their pathophysiology, diagnostic strategies, treatments, and future perspectives. It highlights the importance of early and multidisciplinary management to improve outcomes for affected children.