Embodiments of the invention are directed to methods of diagnosing eosinophilic esophagitis (EoE), or remission therefrom in a subject, wherein the methods include applying a sample from the subject to a diagnostic panel that contains selected markers for EoE, analyzing to obtain relatedness information relative to an EoE cohort and making a determination as to the EoE status of the subject, wherein an analysis indicating grouping with an EoE cohort or a quantitative score similar to that of an EoE cohort are indicative of EoE in the subject. Embodiments of the invention are also directed to methods of monitoring the pathological development or medical prognosis of EoE in a subject.