Magnesium is a trace element that is closely linked to thyroid function and autoimmune thyroiditis. Numerous chronic disorders are also linked to low serum magnesium levels; however, it is unclear how its level relates to the development of autoimmune thyroiditis. In the present study, we evaluated the relationship between Hashimoto’s thyroiditis (HT) and serum magnesium levels in 104 patients; 52 with low and 52 with normal serum magnesium levels. Patient records were retrospectively evaluated and the demographic data, serum levels of thyroid-stimulating hormone, anti-thyroid peroxidase antibody (TPOAb), anti-thyroglobulin antibody (TGAb) and serum magnesium levels were recorded. Patients with low magnesium levels were found to have higher levels of TPOAb, TGAb and radiological evidence of HT when compared to those with normal magnesium levels (P = 0.001, P = 0.007, and P = 0.001, respectively). In logistic regression analysis, ultrasonographic HT findings were found to be significantly more common in the magnesium deficient group (P = 0.001). Serum magnesium level of 0.72 mmol L-1 was determined to be the appropriate cut-off point for the presence of HT ultrasonographic findings with 68.9% sensitivity and 64.4% specificity. As a result, in the present study, low serum magnesium levels were found to be associated with significantly higher incidence of ultrasonographic findings of HT, which may suggest that adequate magnesium supplementation may be an independent protective factor against Hashimoto's thyroiditis.