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BACKGROUND Functional dyspepsia is a common, troubling, and usually chronic disorder. Although the merit of using pathological assays has not been confirmed, medications affecting eosinophils may result in some improvements. Disseminated distribution of mast cells may also be an essential factor. Given the probable associations and lack of evidenced-based data, this study was conducted to comparatively investigate the number of eosinophils and mast cells in the duodenum in functional dyspepsia patients and healthy controls. METHODS In this case-control study, 150 consecutive subjects in Kerman, Iran, were enrolled in 2015 and 2016; the subjects consisted of 100 patients with functional dyspepsia and 50 asymptomatic healthy controls. Samples from the two groups were compared for the number of eosinophils, mast cells, and Helicobacter pylori presence by grasp biopsy. RESULTS The mean number of mast cells significantly differed between the groups (P = 0.001), but the eosinophil count was similar (p > 0.05). Female gender, no opioid use, and H. pylori may increase mast cell count (p < 0.05). CONCLUSION Overall, the mast cell count was significantly different between people with functional dyspepsia and people without it, but the eosinophil count in the two groups was similar. [ABSTRACT FROM AUTHOR]