Objective: To evaluate the potential of omega-3 polyunsaturated fatty acid supplement as an effective, safe and inexpensive medicine for the treatment of recurrent aphthous stomatitis. Methods: In this double-blind clinical trial, 50 patients with recurrent aphthous stomatitis were randomly divided into the omega-3 group and placebo group. Patients in the omega-3 group received 1000 mg omega-3 group capsules (Daroupakhsh Company, Tehran, Iran) for 6 months; while those in the placebo group received placebo capsules with the same instructions. The pain, size, duration and recurrence rate of ulcers were recorded in each follow-up phase. Follow-up was done weekly in the first month of drug prescriptions and then monthly in the next 5 months. The data were analysed with SPSS-20 through the Mann-Whitney test to compare the groups with respect to each variable and the Wilcoxon and Friedman tests to compare the groups over time. Values were significant at P 0.05. Results: In the omega-3 group, pain was lessened from 4.96 to 3.04, irritation was reduced from 5.88 to 4.00 (P = 0.0627) and the size of ulcers was decreased from 2.30 to 1.48 mm (P = 0.062). No significant change was observed in the aforementioned variables in the placebo group. Moreover, the number of ulcers indicated a significant reduction in the fourth, fifth and sixth months in comparison with the placebo group (P = 0.00). Conclusion: The recurrence of ulcers in the omega-3 group showed a significant decrease in the fifth and sixth months compared with the placebo group (P 0.05). The current study indicated that omega-3 consumption decreased the symptoms of recurrent aphthous stomatitis. Palabras clave: omega-3, recurrent aphthous stomatitis, treatment