Background. Violation of the integrity of the histohematologic barriers (blood-brain, blood-testis, blood-ocular, blood-labyrinth, blood-thyroid) leads to autoimmune damage to these organs. One of the manifestations of the latter is autoimmune thyroiditis, the structural and quantitative changes of which can be more informatively accurately assessed by polarization biomedical optics. The purpose of the study was to substantiate the possibility of using polarization biomedical optics methods in the diagnosis of autoimmune thyroiditis based on the use of pathophysiological analysis of blood-brain barrier integrity disorders. Materials and methods. Two groups of patients were studied: control group 1 — healthy donors (n = 51), study group 2 — people with autoimmune thyroiditis (n = 51) who underwent a puncture biopsy of the thyroid gland for diagnostic purposes. Instrumental laser methods were used: polarization, interference, multifractal. The statistical parameters of polarization ellipticity maps, polarization ellipticity of phase and multifractal spectra of digital microscopic images of native thyroid histological sections in patients with autoimmune thyroiditis were quantified: mean, dispersion, asymmetry, and kurtosis. The probability of differences compared to the controls, taken as 100 %, was evaluated using the Student’s parametric test (p < 0.05). Results. A significant increase in the mean and variance at inhibition of the asymmetry and kurtosis of polarization ellipticity, as well as in the mean and variance at reduction of the asymmetry and kurtosis of polarization ellipticity of phase digital microscopic images of thyroid native histological sections was revealed. There were a significant increase in dispersion and a decrease in the asymmetry and kurtosis of multifractal spectra of polarization ellipticity maps of digital microscopic images of native histological sections. Conclusions. A significant increase in the biophysical optical parameters of digital microscopic images of thyroid native histological sections from patients with autoimmune thyroiditis was found due to the growth of connective tissue in the interstitium as a result of an autoimmune inflammation. There was a significant inhibition of the asymmetry and kurtosis of the ellipticity of polarization of phase digital and multifractal spectra of polarization ellipticity maps of microscopic images of native histological sections in patients with autoimmune thyroiditis due to a decrease in the amount of colloids as a crystalline component caused by damage to the blood-thyroid barrier.