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To evaluate the utility of activated mucosal mast cells (MC) in the differential diagnosis of eosinophilic esophagitis (EE) and gastroesophageal reflux disease (GERD).Intraepithelial eosinophils and MC were quantified in esophageal biopsies from 25 children with EE, 22 children with GERD and 22 controls. MCs were identified by immunohistochemistry for MC tryptase, whereas MC activation status was evaluated by immunohistochemistry for immunoglobulin E (IgE) and by electron microscopy.Esophageal biopsies from patients with EE showed higher intraepithelial eosinophil counts (55 ± 27.5 vs 6.9 ± 9.7, P < 0.0001) and MC counts (26.3 ± 12.7 vs 7.8 ± 8.9, P < 0.0001) than those from patients with GERD. Almost all EE biopsies (24 of 25 patients; 96%) contained IgE-bearing cells compared with 9 of 22 (41%) GERD biopsies (P < 0.001). GERD biopsies with intraepithelial eosinophil counts >7/high-power field (suggesting an allergic component) contained IgE-bearing cells in 6 of 7 (86%) cases compared to 3 of 15 (20%) cases with eosinophil counts <7/h.p.f (P < 0.01). No intraepithelial eosinophils, MC or IgE-positive cells were present in controls. Electron microscopy confirmed the presence of intraepithelial MC and changes in cytoplasmic granules indicative of MC and eosinophil activation.Intraepithelial MC counts and IgE-bearing cells may help to differentiate EE and GERD and to define a subset of GERD patients in which an allergic component is present. The findings support a role for a MC-mediated hypersensitivity reaction in the pathogenesis of EE.