Eating disorders are one of the most common chronic conditions in adolescents. The clinical symptoms can mimic those of other chronic diseases including gastrointestinal and endocrine disorders. However, an eating disorder can coexist with another chronic disease, making the diagnosis and management of both conditions challenging. This Review describes what is known about eating disorders in adolescents with chronic gastrointestinal and endocrine diseases, focusing on coeliac disease, inflammatory bowel disease, diabetes, and thyroid disorders. The prevalence and onset of each condition during adolescence is discussed, followed by a description of the associations among the conditions and eating disorders. We also discuss management challenges posed by the coexistence of the two conditions. When both diseases coexist, a multidisciplinary approach is often needed to address the additional complexities posed.