Objective: Previous trials show that selenium could be a very useful tool in control and treatment of autoimmune thyroid diseases. In this cross-sectional study, through a survey, we aim to evaluate Portuguese endocrinologists' perception and pattern of prescription of selenium supplements in these diseases and verify its agreement with current guidelines. Methods: The endocrinologists registered in the Portuguese Medical Association were sent an email with a web-based questionnaire, regarding their knowledge and use of selenium supplements in thyroid autoimmune pathology. Results: A total of 105 physicians (33% of the total) submitted the survey. The selenium serum concentration in the general population was unknown to 80% of respondents. Over a third of respondents have never prescribed selenium in Autoimmune Thyroid Disease. However, 89% are not afraid of recommending it, and 61% indicate Graves’ Orbitopathy as the pathology they would supplement. In Hashimoto’s Thyroiditis, 36% of respondents use selenium occasionally or frequently, and this percentage rises to 60% in Graves’ Disease. Conclusions: Although recommendations only encompass mild Graves’ Orbitopathy, selenium is prescribed across the spectrum of autoimmune thyroid diseases, probably due to recent studies that consistently show improvement of biochemical hallmarks in these patients. Further investigation is required on the impact of selenium supplements on primarily clinical outcomes and to identify disorders and/or patients who will benefit the most. Also, there is still insufficient knowledge on this field in the medical community, and evidence-based practice should continue to be promoted by endocrinology societies.