BACKGROUND: Dyspepsia is a common symptom with a broad differential diagnosis and complex pathophysiology which annually affect about 25% of the general population. Results of Helicobacter pylori eradication in the patients with dyspepsia symptoms in the different studies are controversy. Aim of the study was to evaluate the effect of Helicobacter pylori eradication in the patients with functional dyspepsia. METHODS: In order to doing the clinical trial study, demographic and clinical symptoms of the patients that referred to the gastroenterology center of the Ilam County from 1391 to 1392 was recorded in a standard questionnaire (including criteria of ROM III). Overall 120 patients with dyspepsia were selected and divided into two groups of "control" and "treatment". Helicobacter pylori presence was confirmed by stool antigen test in all of the patients. Selected patients were randomly divided into two groups. Standard therapy for the Helicobacter pylori eradication was done for two weeks periods in the one group. Then in this group antacid medication (morning and night) was continued. Four weeks treatment with antacid medication (morning and night) was performed for second group (control) and then both groups were treated with antacid for three month and both groups were finally evaluated with same questionnaire. RESULTS: The mean age of patients was 32 years; 55.8% of the patients were female. The most prevalent symptoms of functional dyspepsia (25.7%) were in the age groups of 16-34 years and 35-43 years. All of dyspepsia symptoms in the both groups of cases (Helicobacter pylori standard treated) and control (treated with antacid) decreased after treated. However, this reduction in all symptoms was not significant except for epigastric pain and vomiting. CONCLUSIONS: Helicobacter pylori eradication has a little effect in improving of the functional dyspepsia syndrome and the effect was justly seen in the symptoms of epigastric pain and vomiting.