Purpose: Oral mucositis (OM) is the most frequent side effect of radiation. Selenium deficiency leads to increased levels of free oxygen radicals and the selenium level tends to fall during radiotherapy. Hence, in this double-blind randomised controlled clinical trial, the effect of selenium was assessed in patients receiving radiation. Materials and Methods: Patients with head and neck cancer who were candidates to receive radiation were instructed to use selenium 200 mcg tablets twice daily. The grade of OM was evaluated by the World Health Organization (WHO) grading system on a weekly basis. The selenium level was measured at baseline and at the end of the radiation. Results: Seventy-one patients with head and neck cancer (37 in the selenium group, 34 in the placebo group) were enrolled in the study. The cumulative incidence of OM (grade 1–4) was 97.3% in the selenium and 100% in placebo group (p value: 0.79), and difference in the mean serum selenium level at the end of radiation was not statistically significant between the two groups (p value 0.24) Conclusion: Selenium supplementation does not appear to affect the selenium level as well as the severity and duration of OM. It is supposed that higher doses may be effective in the prevention of RT-mucositis. This trial was registered in the Iranian Registry of Clinical Trials accessible at www.irct.ir (ID No. IRCT2014072718612N1) Keywords: selenium, oral mucositis, head and neck cancer, radiation, concurrent chemotherapy, prevention