Objective: Helicobacter pylori is a main etiological parameter in chronic active gastritis, gastric duodenal ulcers and gastric malignancy. Particular polyunsaturated fatty acids (PUFA) play roles in inhibitory effect on bacterial propagation. Therefore, this study investigated the protective effects of PUFAs against oxidative stress in patient infected with H. pylori with dyspeptic symptom. Methods:This study is a double blind clinical trial whose target population was 34 patients infected with H. pylori with dyspeptic symptom. Patients were divided into two groups. The first group was treated with standard therapy without supplement (control), and the second group was treated with Standard Therapy and PUFAs supplement, ω-3, ω-6 and ω-9 (case group) for 2 weeks. Two biopsies from Antrum and body of stomach of all patients were collected before and after the treatment. The biopsy samples were used for quick urease test and measurement of Superoxide Dismutase, Glutathione Peroxidase, and total antioxidant capacity. Results:In gastric mucosa mean levels of total capacity antioxidant were significantly increased in case group comparing with control group. Also, the mean of superoxide dismutase enzyme activity and glutathione peroxidase activity increased significantly in case group compared with control group (p value <0.001). Conclusion:The findings revealed that administration of PUFAs supplement can increase total antioxidant capacity and activity of antioxidant enzymes in patients infected with H. pylori.