Background: Although in many studies, the relationship between autoimmune hypothyroidism (Hashimoto) and Vitamin D deficiency was shown, no research has been performed on the role of vitamin D in non-autoimmune hypothyroidism.Methods: This was a case-control study in Endocrinology clinic of Jahrom (south of Iran). The patients with Hashimoto (n=633) and non-Hashimoto hypothyroidism (n=305), along with a control group (n=200) were evaluated. 25(OH) D level, T3 and T4 levels were studied and Anti TPO and Anti TG tests were performed. The results of vitamin D level were analyzed and interpreted using SPSS in terms of the cause of hypothyroidism (immune and non-immune).Results: The results of the study showed a significantly lower level of vitamin D in both immune and non-immune Hashimoto’s thyroiditis (HT) in comparison to healthy controls (P<0.05). We observed a significant inverse correlation between the vitamin D and TGAb level (p=0.001, r=-0.261) and a direct correlation of vitamin D with TSH level (p=0.008, r=0.108) in Hashimoto thyroiditis patients.Conclusion: Finally, the results indicated that non-autoimmune hypothyroidism, as well as HT, is associated with vitamin D deficiency. The role of vitamin D deficiency in Hashimoto thyroiditis was thought to be in the association of higher autoantibody (TGAb) level; while, there should be further studies determining vitamin D deficiency's role in non-immune hypothyroidism.