Esophageal biopsies are essential for confirming the presence of EoE, since there are no symptoms or blood tests that can accurately diagnose EoE and rule out other possible disorders. Biopsies are taken during an upper endoscopy, and should be taken from multiple locations in the esophagus. The reason for multiple esophageal biopsies is that EoE can be a patchy disease so one or two biopsies can miss this diagnosis. Furthermore, the biopsies should be taken while a person is on adequate anti-reflux medications to prevent acid reflux disease confusing the diagnosis. If anti-reflux medications were not being regularly taken, a pH or impedance study may be used to identify any underlying acid reflux.

Theses biopsies should be evaluated by a pathologist who has experience with eosinophilic gastrointestinal disorders. They need to be examined under a microscope to look for the presence of white blood cells called eosinophils which is the hallmark of this disease. A common research criteria for diagnosing EoE is that the PEAK eosinophil counts of more than 15 to 20 eosinophils seen on a single high powered microscopic field indicates that the diagnosis of eosinophilic esophagitis likely. In addition other microscopic findings may be seen to give clues to this diagnosis. A pattern of eosinophilic inflammation of the lower esophagus with relative sparing of the upper esophagus could be more suggestive of reflux disease, since reflux is considered to be a continuum of inflammation, with signs of inflammation usually decreasing as you proceed higher up in the esophagus. Although a diagnosis should not be made solely by the distribution of inflammation seen on biopsies.