This study aimed to evaluate the efficacy of Nigella sativa seed oil mixed with honey in treatment of patients with functional dyspepsia. Seventy patients diagnosed as functional dyspepsia according to ROME III criteria and confirmed by upper gastrointestinal endoscopy were selected and randomly divided in to two equal groups. Patients with organic causes of dyspepsia, peptic ulcer disease, inflammatory bowel disease or pure gastroesophageal reflux disease were excluded from the study. Patients in both groups were instructed to take 5 ml of Nigella sativa seed oil mixed with honey or placebo, 3 times per day after their meal. Patients in both groups also received 40 mg famotidine drug daily during the study.The dyspepsia severity as a primary out come and presence of H. pylori infection and different domains of health survey as secondary outcome were determined in both groups prior to and following 8 weeks of the intervention.