Selenium deficiency may play an important role in the initiation and progression of autoimmune thyroid disease. To compare serum selenium (s‐Se) values in patients with newly diagnosed autoimmune thyroid disease and controls from the Danish population. S‐Se was measured in triplicate by a fluorimetric method. Patients with newly diagnosed Graves’ disease (GD) (n = 97) or autoimmune overt hypothyroidism (AIH) (n = 96), euthyroid subjects with high serum levels of thyroid peroxidase antibody (TPO‐Ab) (TPO‐Ab > 1500 U/ml, n = 92) and random controls (n = 830). Differences in s‐Se values. S‐Se was lower in patients with GD than in controls (mean (SD), GD: 89·9 μg/l (18·4); controls: 98·8 μg/l (19·7), P < 0·01). This was confirmed in a multivariate logistic regression model adjusting for age, sex, mineral supplements, smoking, geographical region and time of sampling (P < 0·01). In a linear model, s‐Se was similar in patients with AIH (mean (SD): 98·4 μg/l (24·9)) and in controls (P = 0·86). In the multivariate model however, s‐Se was marginally lower in patients with AIH compared to controls (P = 0·04). There was no significant difference in s‐Se between euthyroid participants with high TPO‐Ab and random controls (linear: P = 0·97; multivariate: P = 0·27). Patients with newly diagnosed GD and AIH had significantly lower s‐Se compared with random controls. Our observation supports the postulated link between inadequate selenium supply and overt autoimmune thyroid disease, especially GD.