Thyroglobulin is a major autoantigen to which autoimmune response, destroying the thyroid gland in Hashimoto's thyroiditis, is directed. To detect a pathological autoimmune response to thyroglobulin, as well as the successful induction of experimental autoimmune thyroiditis, thyroglobulin carrying thyroiditogenic epitopes is necessary. It is not known which features of thyroglobulin structure determine the presence of thyroiditogenic epitopes and can serve as markers of their presence. We compared structure of thyroglobulin bearing thyroiditogenic epitopes (freshly isolated thyroglobulin) and thyroglobulin which had lost thyroiditogenic epitopes (lyophilized thyroglobulin). Fourier-transform infrared (FTIR) spectroscopy was used to elucidate the structure of thyroglobulin. The markers indicating the presence of thyroiditogenic epitopes on thyroglobulin are the vibrations of diiodotyrosine, monoiodotyrosine/diiodotyrosine relation in the range of 0.24-0.43 (95% confidence interval) and relatively high (>
32%) α-helix content. The loss of thyroiditogenic epitopes on thyroglobulin is associated with a weakening or complete disappearance of diiodotyrosine oscillations and a decrease in the proportion of α-helices in secondary structure. Thyroglobulin extracted with phenylmethylsulfonyl fluoride (PMSF) added is characterized by the same relatively high monoiodotyrosine/diiodotyrosine relation and low proportion of alpha helices as thyroglobulin without thyroiditogenic epitopes. Therefore, serine protease inhibitor PMSF is not suitable for extraction of native thyroglobulin bearing thyroiditogenic epitopes. FTIR spectroscopy can be used to detect thyroiditogenic epitopes on thyroglobulin.