The burden of endoscopy in eosinophilic esophagitis (EoE) is great, with many patients undergoing multiple endoscopies to verify treatment success. The gold standard for monitoring disease activity EoE is histologic evaluation and eosinophil enumeration. Although symptoms have been less reliable to track disease activity, multiple noninvasive methodologies are being investigated to sample the esophageal tissue. A better understanding of disease phenotype, genotype, and transcriptome may lead to more personalized approaches to diagnostics and therapeutics in EoE.