In recent years the intestinal microbiome and its interaction with the brain has aroused a growing interest. The findings gained in the course of this research are of great relevance not only to basic scientists but also to clinicians, as studies suggest an association between an altered microbiome and various somatic (e.g. chronic inflammatory intestinal diseases, obesity and diabetes) as well as psychiatric diseases (e.g. anxiety disorders, depression). In addition to a direct influence of the microbiome on the brain and behavior, various mechanisms seem to be relevant, including altered energy intake from food, hormonal changes, probably increased intestinal permeability as well as inflammatory and immunological processes. Anorexia nervosa (AN) is the third most common chronic disease in adolescence and has the highest mortality rate among all mental disorders. In addition to extremely restrictive eating habits, weight loss and comorbid anxiety and depression symptoms, endocrine changes and an increased autoimmune and inflammatory response are characteristic. Since AN is particularly strongly linked to eating behavior and nutrition, research into the microbiome seems very promising, especially with respect to this disease. This article gives a first insight into the underlying processes that play a role in gut-brain interaction in the context of AN and summarizes the previous empirical findings on this topic. Finally, an outlook on future research and possible implications for the therapeutic practice and treatment of AN is given.