Eosinophilic esophagitis (EE) is a newly recognized disease, which has largely been called idiopathic EE, emphasizing the poor understanding of its pathogenesis. EE is a severe disease of the esophagus characterized by an accumulation of eosinophils in the esophageal mucosa, and is highly associated with atopic disease. Nevertheless, the nomenclature “eosinophilic esophagitis” describes only the tip of the iceberg of a complex disorder, as the pathogenesis of EE involves multiple tissues, cell types, and genes, and derives from complex genetic and environmental factors. This article defines the fundamental knowledge available to date that characterizes the mechanisms by which certain etiological factors cause EE, reviewing human studies, murine models, and recent knowledge regarding the involvement of environmental, cellular, molecular, and genetic factors in the development of EE.