Introduction: Goiter is a common problem in the world; however, it is more prevalent in countries with iodine deficiency. Goiter has different etiologies while one of them is Hashimoto’s thyroiditis. Selenium is a trace element that has different important effects in the body. It has also some effects in the thyroid. Objectives: This study aimed to evaluate the effect of selenium intake on goiter size and the correlation with goiter type. Patients and Methods: In prospective observational study, 20 patients with Hashimoto’s goiter and 40 patients with non-Hashimoto’s goiter were evaluated for thyroid sizes. The nodule sizes were else evaluated. After the first evaluation, daily selenium supplement (200 mg) was prescribed for all patients for six months. After this time, the sizes of goiter and nodules were measured again. Results: Results showed that the size of both goiter lobes in both Hashimoto’s and non-Hashimoto’s groups was significantly reduced before and after selenium intake (P<0.001). The reduction rate in left lobe size in patients with Hashimoto’s goiter was 50.73% and in nonHashimoto’s goiter patients was 20.89% (P<0.001). The reduction rate in right lobe size in patients with Hashimoto’s goiter was 53.37% and in non-Hashimoto’s goiter was 20.46 (P<0.001). Conclusion: We conclude that administration of selenium is effective in reducing the size of the goiter.