Children who have eosinophilic esophagitis require comprehensive evaluation before treatment and ongoing assessment during treatment. When completed at the appropriate times and under well-controlled circumstances, investigation yields the correct diagnosis, assures recognition of sequelae or recurrence of the inflammation, or confirms whether therapy has been effective. Proper management of each child depends on compulsive follow-up until all of the therapeutic goals have been achieved and the child is on a stable regimen without esophageal inflammation. This article summarizes the issues facing the patient and the physician during this process.