Background: Hashimoto's thyroiditis (HT) is a known autoimmune disease of the thyroid gland and is usually associated with cognitive disorders. Aim: To investigate the utility of brain magnetic resonance spectroscopy (MRS) and diffusion tensor imaging (DTI) in the detection of any metabolic or microstructural changes in HT patients who have normal conventional brain MRI, in correlation to thyroid peroxidase antibodies (TPOAb) levels and disease duration. This casecontrol study involved 40 patients with HT and 20 healthy controls. All the patients were euthyroid at the examination time and underwent hormonal assessment (TSH, T3, T4), TPOAb titer, brain MRS, and DTI. Correlations between MRS ratios, DTI values, TPOAb titer, and disease duration were performed. Results: Lower NAA/Cr and higher mI/Cr ratios in posterior cingulate gyrus (PCG) and parietal white matter (PWM) were observed in patients than in healthy controls (p= 0.001). A lower value of fractional anisotropy (FA), radial diffusivity (RD), and higher mean diffusivity (MD), and axial diffusivity (AD) were observed in patients versus control groups. Moderate positive correlation between disease duration and mI/Cr in PCG and PWM areas, and RD in the corpus callosum (p= 0.021, 0.013, 0.025, respectively), a moderate negative correlation between TPOAB and NAA/Cr in PCG, FA in the posterior limb of the internal capsule (PLIC) (r=− 0.536, p= 0.001, r= -0.436, p= 0.028 respectively). Conclusion: Brain MRS and DTI showed metabolic and microstructural changes in neurocognitive-related regions in patients with HT, which will help in understanding the concomitant neurocognitive deficits and disease management.