Eosinophils are potent innate immune cells that home to the gastrointestinal tract where they participate in host immunity to luminal pathogens, and help to maintain intestinal epithelial homeostasis. However, these cells are now recognized to have key functions in the pathogenesis of numerous other disorders of the gastrointestinal tract, including primary eosinophilic gastrointestinal disease, common functional conditions, such as dyspepsia, and also in gastrointestinal disorders in patients with allergic disease. We are just beginning to understand the potential pathological role of eosinophils in gastrointestinal disease, and it is increasingly likely that gastroenterologists and histopathologists will need to account for the presence of gastrointestinal eosinophils and relate their presence to gastrointestinal symptoms. This Review discusses the role of gastrointestinal eosinophils in health and disease, including their associations with functional and allergic disorders.