BACKGROUND AND AIM: Dietary factors and immune dysfunction may induce symptoms in patients with functional dyspepsia (FD). The aim of the study was to evaluate whether gluten consumption impacts symptom onset in patients with FD and to evaluate for possible histologic alterations in the duodenum of patients with FD. METHODS: We prospectively enrolled 101 patients newly diagnosed with FD and 31 asymptomatic controls. Specific FD symptoms and gluten consumption patterns were evaluated by self-reported questionnaires. Tight junction protein (claudin-1) expression and presence of intraepithelial lymphocyte (IEL) infiltration in the bulb (D1) and second portion (D2) of the duodenum were assessed by immunohistochemistry. RESULTS: Wheat bun consumption had higher frequency (P = 0.047) and increased average consumption (P = 0.01) scores in patients with FD compared with the control group. Of the 101 patients with FD, early satiety (P = 0.03) was associated with increased wheat bun consumption frequency score. On histologic evaluation, claudin-1 expression was decreased in D1 (0.003 ± 0.001 vs 0.012 ± 0.002, P = 0.003) and D2 (0.002 ± 0.0004 vs 0.012 ± 0.001, P < 0.001), while duodenal IEL counts were increased in D1 (15.5 ± 7.8 vs 3.1 ± 2.5, P < 0.001) and D2 (20.6 ± 7.7 vs 5.8 ± 3.4, P < 0.001) among patients with FD compared with the control group. Finally, Helicobacter pylori infection was associated with increased IELs in D1 (20.6 ± 7.0 vs 14.2 ± 7.4, P = 0.001) among patients with FD. CONCLUSIONS: Among patients with FD, gluten-rich food may lead to symptom onset, specifically early satiety. Intestinal epithelial barrier dysfunction characterized by decreased claudin-1 expression and mucosal immune activation demonstrated by IEL infiltration may contribute to the pathogenesis of FD.