Eosinophilic gastroenteritis(EGE) is a rare immune-mediated disorder marked by gastrointestinal mucosal dysfunction and eosinophil inflammation. We evaluated mucosal dysfunction and intestinal permeability in two patients using endoscopy, histology, and probe-based confocal laser endomicroscopy (pCLE) at diagnosis and after five weeks of corticosteroid therapy. Baseline histology confirmed marked eosinophilic infiltration, while pCLE revealed interstitial leakage and increased epithelial permeability even in endoscopically and histologically normal mucosa. Treatment induced clinical, endoscopic and histologic remission but pCLE continued to detect subtle, persistent barrier defects in regions with normalized endoscopy and histology, suggesting residual subclinical disease. These findings suggest that achieving “functional healing” of the gut barrier may represent a critical, new therapeutic frontier.