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BACKGROUND AND PURPOSE Hashimoto's thyroiditis (HT) is a type of autoimmune thyroid disease. Diffusion tensor imaging (DTI) can evaluate microstructural brain involvement in various diseases. We aimed to investigate whether there were any DTI differences in patients with HT, and the relationship between DTI values and disease duration time and thyroid peroxidase antibodies (TPOAb) levels. METHODS We prospectively included 36 patients with HT (mean age 41.6 ± 13.8 years, range 18‐64 years) and 18 age and sex‐matched healthy control subjects (mean age 41.6 ± 13.1 years, range 18‐63 years). All patients were euthyroid at the time of imaging. Fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD) values of 15 distinct neuroanatomical locations were measured and compared. RESULTS FA values of the patients with HT were lower in cingulum, globus pallidus (GP), cerebellar white matter (CWM) than the control (P = .019, .002, and <.001, respectively). MD values of the CWM in patients were higher than the control (P = .008). AD values of patients with HT were lower in the cingulum, posterior limbs of the internal capsule, GP, and putamen (P = .038, .038, .030, and .045, respectively). RD values of cingulum and CWM in HT were higher than controls (P <.001 and P = .011, respectively). There was a negative relationship between the FA values of PLIC and a positive relationship between the MD values of the corona radiata and TPOAb levels were detected. CONCLUSIONS The current DTI study presented microstructural changes in the neurocognitive‐related areas that may be related to accompanying neurological findings in HT.