Eosinophilic esophagitis (EoE) shares many features with other atopic diseases such as asthma, including heterogeneity in its presentation, natural history, and response to treatment. Clinical and molecular evidence suggests that different eosinophilic esophagitis patient phenotypes and endotypes exist. Phenotypic variations in EoE include the age of onset, degree of atopic comorbidity, response to different forms of therapy, and disease severity, among others. Biomarkers that may provide insight into the mechanisms of EoE for defining endotypes include the presence or absence of systemic Th2 inflammation, genetic risk factors, and histologic findings.