This study aimed to evaluate the relationship of esophageal epithelial permeability with mast cell infiltration and IgG4 deposits as well as chemokine levels in eosinophilic esophagitis (EoE) patients before and after treatment. Biopsies from controls and EoE patients before and after treatment were analyzed. Hematoxylin and eosin staining was used to show eosinophil infiltration. Paracellular permeability of the esophageal epithelium was assessed using surface biotinylation. Immunohistochemical staining was performed to examine mast cell infiltration and IgG4 deposits. Gene expression of chemokines was evaluated by qRT-PCR. Esophageal epithelial infiltration of mast cells, IgG4 deposits, and permeability were significantly increased in EoE patients. Levels of interleukin-13, calpain-14, and eotaxin-3 mRNAs were significantly upregulated, while filaggrin, serine peptidase inhibitor Kazal type 7 (SPINK7), and involucrin mRNAs were significantly downregulated in EoE patients. In patients achieving histologic remission diagnosed by eosinophil counts, a subset of EoE patients with unchanged permeability after treatment showed increases in mast cell infiltration, IgG4 deposits, and interleukin-13, calpain-14, filaggrin, and SPINK7 expression, with decreased eotaxin-3 and involucrin. Other EoE patients with decreased permeability displayed decreased eotaxin-3, involucrin, and mast cell infiltration, no IgG4 deposits, and increased IL-13, calpain-14, filaggrin, and SPINK7. Increased permeability of the esophagus in EoE patients without eosinophil infiltration after treatment was associated with mast cell infiltration and IgG4 deposits.