Several mechanisms have been proposed to explain the symptoms of functional dyspepsia but actual pathogenesis is still poorly understood. Recent studies support duodenal abnormality to be the most important causal link to explain symptoms and to understand abnormal pathophysiology of functional dyspepsia. The aim of this prospective observational study is to compare eosinophil count in duodenal mucosa between patients with functional dyspepsia and control subjects without dyspepsia and was done at the department of Gastroenterology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh from December 2015 to December 2016. Total 42 patients of functional dyspepsia based on Bangla validated version of ROME III criteria and 42 controls who were referred for upper gastrointestinal endoscopy for reasons other than dyspepsia were included. Biopsy specimens were collected from the second part (D2) of the duodenum of all participants. Eosinophil count was quantitatively evaluated by hematoxylin and eosin staining and expressed in numbers per 5 HPF. Significantly increased duodenal eosinophil count was found in functional dyspepsia group than non dyspeptic patients (22.78±08.78 vs. 14.90±10.70, p=0.001). Higher duodenal eosinophil count was found in patients with postprandial distress syndrome. Increased duodenal eosinophil count was found in patient of functional dyspepsia. It requires further large scale multicenter studies to establish duodenal eosinophilia as a biomarker of functional dyspepsia.