Epidermal differential complex (EDC) proteins, such as filaggrin, involucrin, and loricrin, play key roles to protect the mucosal surface against invading pathogens. Eosinophilic esophagitis (EoE) is an allergic gastrointestinal disease that features eosinophilic infiltration of esophageal mucosa, though the function of EDC proteins in its pathogenesis remains unknown. The aim of this study was to investigate possible differences of EDC protein expression in the epithelium of the esophagus, pharynx, and tongue. Furthermore, we examined that expression in esophageal specimens obtained from patients with EoE. For evaluating EDC protein expression in epithelium from different locations, we enrolled 72 patients who underwent surgical resection for esophageal, pharyngeal, or tongue squamous cell carcinoma. Pathological samples were used for analysis of expression by immunohistochemistry. In addition, samples were obtained from 10 patients with EoE and 11 healthy subjects, and compared for esophageal epithelial expression of EDC proteins. In epithelium samples obtained from the esophagus, pharynx, and tongue, the presence of EDC proteins was confirmed by immunohistochemistry analysis findings, though the expression patterns were notably different in comparison to that in epidermis samples. In EoE patients, the expression of involucrin was dramatically down-regulated in esophageal mucosa, whereas down-regulation of filaggrin and loricrin did not reach a statistically significant level. EDC protein expression was clearly detected in pharyngoesophageal epithelium samples, while that of involucrin alone was markedly reduced in patients with EoE.