Functional Dyspepsia (FD) is one of the most common functional gastrointestinal disorders, which remains as a great burden to the healthcare system. Although the etiology and the pathogenesis of FD are not yet completely clear, the duodenum has been suggested as the key position of FD. In order to examine the association between food allergy and duodenal mast cells in patients with FD, the current study performed a retrospective review on 48 patients. Mucosal tissue specimens were obtained from the duodenal bulb and descending duodenum. IgG antibody in the serum was then detected using enzymelinked immunosorbent assay. Toluidine blue staining was used to identify mast cell counts and degranulation rates. According to the results of Pearson rectilinear correlation analysis, mast cells were significantly increased in patients with FD compared with the number in healthy volunteers (P<0.01). Degranulation ratios (%) of mast cells in patients were also significantly increased (P<0.01). Positive rates of IgG to certain types of food in patients with postprandial distress syndrome and epigastric pain syndrome were significantly increased, and the kinds of food allergen-specific antibodies and scores of IgG in the serum were significantly increased compared with the controls (P<0.01). Allergen-specific IgG scores and types demonstrated positive correlations with cell counts (r=0.247, P=0.038; r=0.243, P=0.041) and degranulation rates (r=0.307, P=0.011; r=0.326, P=0.007) of mast cells. Thus, these findings suggested that food allergy in patients with FD may increase cell counts and degranulation ratios of duodenal mast cells.