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Abstract Background: Vitamin D level is thought to be involved in many diseases, and is thought to be found in autoimmune thyroid diseases. Vitamin D receptor polymorphism is now emerging as a cause of vitamin D deficiency in many diseases in all populations. Aim: The current case-control study aimed at assessment of vitamin D level and vitamin D receptor polymorphism in hypothyroid patients and its effect on hypothyroidism and to find a causal relation between vitamin D and hypothyroidism. Subjects and methods: The current study included 35 hypothyroid patients and 35 matched unrelated healthy controls. Genotyping was performed by using real time-PCR (TaqMan probes). Results: The study showed that vitamin D level is lower in hypothyroid patients than in control subjects. It is also inversely related to TSH, HOMA-IR, level of anti-TG and anti-TPO. VDR polymorphism has no relation to TSH and vitamin D levels. Conclusion: The study confirmed association of vitamin D deficiency with hypothyroidism, autoimmunity, increased volume, nodularity and vascularity of thyroid gland in hypothyroid patients as well as increased HOMA-IR. The study proved no association between VDR polymorphisms with both vitamin D levels and TSH levels |