BACKGROUND: Functional dyspepsia is characterised by chronic symptoms of post-prandial distress or epigastric pain not associated with defined structural pathology. Increased peripheral gut-homing T cells have been previously identified in patients. To date, it is unknown if these T cells were antigen-experienced, or if a specific phenotype was associated with FD. OBJECTIVE: This study aimed to characterise T cell populations in the blood and duodenal mucosa of FD patients that may be implicated in disease pathophysiology. METHODS: We identified duodenal T cell populations from 23 controls and 49 Rome III FD patients by flow cytometry using a surface marker antibody panel. We also analysed T cell populations in peripheral blood from 37 controls and 61 patients. Where available, we examined the number of duodenal eosinophils in patients and controls. RESULTS: There was a shift in the duodenal T helper cell balance in FD patients compared to controls. For example, patients had increased duodenal mucosal Th2 populations in the effector (13.03 ± 16.11, 19.84 ± 15.51, =0.038), central memory (23.75 ± 18.97, 37.52 ± 17.51, =0.007) and effector memory (9.80±10.50 vs 20.53±14.15, =0.001) populations. Th17 populations were also increased in the effector (31.74±24.73 vs 45.57±23.75, =0.03) and effector memory (11.95±8.42 vs 18.44±15.63, =0.027) subsets. Peripheral T cell populations were unchanged between FD and control. CONCLUSION: Our findings identify an association between lymphocyte populations and FD, specifically a Th2 and Th17 signature in the duodenal mucosa. The presence of effector and memory cells suggest that the microinflammation in FD is antigen driven.