Vitamin D is a modulator of both the innate and adaptive immune system. As vitamin D deficiency was a risk factor for some autoimmune diseases, we aimed to evaluate the serum vitamin D levels in autoimmune thyroid diseases (AITD) including Graves’ disease (GD) and Hashimoto’s thyroiditis (HT) and investigated the association between serum vitamin D levels and AITD. 175 AITD patients including 51 GD, 61 euthyroid HT (mild HT), 63 euthyroid HT patients with hypothyroidism receiving hormone therapy (treated HT) were recruited from the outpatient department. 51 controls were from the physical checkup center of the hospital. 25-Hydroxyvitamin D levels, thyroid function, antithyroid antibodies, IL-4, IL-17, and TNF-α were determined. Compared with the controls, treated and mild HT patients had significantly lower 25(OH)D levels (45.77±3.48 vs. 83.49±6.24 nmol/L, p<0.001) and (55.25±3.88 vs. 83.49±6.24 nmol/L, p<0.001), respectively. However, GD patients had similar 25(OH)D levels (81.77±5.60 vs. 83.49±6.24 nmol/L, p=0.808). Compared to 24.1% controls with prevalent vitamin D deficiency, mild HT and treated HT patients were significantly different (55.4%, p<0.001) and (70.3%, p<0.001), respectively; no difference was seen in the GD patients (22.9%, p=0.797). Serum 25(OH)D levels were not associated with thyroid function, antithyroid antibodies, and serum cytokines IL-4, IL-17, and TNF-α in patients with AITD. We observed relatively low vitamin D level in mild and treated HT patients, while GD patients had similar 25(OH)D levels to those of healthy individuals. Further studies are imperative to explore the complex etiology of vitamin D deficiency in AITD.