AIM: Functional dyspepsia (FD) is a clinical syndrome with chronic gastroduodenal symptoms without noticeable organic or systemic diseases. According to the Rome III consensus, FD can be subdivided into PDS (postprandial distress syndrome) and EPS (epigastric pain syndrome). Neurotransmitters are involved in the development and pathology of FD. However, the expression profiles of neurotransmitters in FD patients are not clear. This study aimed to investigate the expression profile of neurotransmitters in the duodenal mucosa of FD patients. METHODS: A total of 48 FD patients treated at our hospital were included in this study: 23 patients with PDS and 25 patients with EPS. Another 21 healthy volunteers served as normal controls. The duodenal mucosa was biopsied with gastroscopy and examined with immunohistochemical staining against serotonin, substance P, inducible nitric oxide synthase (iNOS), and vasoactive intestinal peptide (VIP). Mast cells were identified with toluidine blue staining. RESULTS: The duodenal iNOS levels were significantly higher in PDS patients than the normal controls (P<0.05). The expression of serotonin, substance P, and VIP did not differ significantly among the groups. Mast cell counts and the percentage of mast cells with degranulation were significantly higher in PDS and EPS patients than normal controls (P<0.001) In addition, iNOS expression levels were positively correlated with percentage of degranulating mast cells (r=0.321, P=0.008). CONCLUSIONS: In conclusion, duodenal iNOS may be involved in the pathogenesis of PDS.