Objective: The purpose of this study was to investigate the benefits of two different Selenium based supplements on patients with chronic autoimmune thyroiditis. Methods: We conducted a prospective study on 50 patients with chronic autoimmune thyroiditis, who were divided into three different treatment groups, one group taking Selenium 100 μg, one Procor T (a combination of Selenium 100 μg and other elements like copper, Zinc and Q10 Conenzyme) and one control group taking Placebo pills. We measured on two follow up visits the antibody levels (anti-thyroidperoxidase- TPO Ab) and offered each patient a standardised questionnaire regarding the thyroid-related quality of life (THYPROro). Results: At the 6 months follow up visit there was a statistically significant decrease in the antibody levels for each treatment group compared to the base levels. The THYPROro questionnaire scores showed an improvement in most aspects regarding the quality of life as well, but there was no significant difference between the placebo and the treated groups in the magnitude of this improvement. Conclusions: Based on our results, we could not identify a certain benefit in improving quality of life with the supplementation of Selenium, as the improvements were at a similar level for the patients who took Placebo pills. Further studies with more patients, as well as taking the Selenium defficiency in consideration (by measuring the basal serum level of Selenium for each patient) would be required to find the target group of patients who could have most benefits of Selenium-based supplementation.