The current study aimed at assessing vitamin D level and vitamin D receptor polymorphism in hypothyroid Egyptian patients and its effect on hypothyroidism and thyroid morphology, also to find a causal relation between vitamin D and hypothyroidism.This case-control study was conducted on 35 hypothyroid patients and 35 matched unrelated healthy controls. Total serum 25-hydroxyvitamin D3 and thyroid antibodies were measured using a human ELISA kit. Genotyping was performed by using real-time PCR. HOMA-IR was also calculated (fasting insulin in mIU/L × fasting glucose in mg/dL/405). All subjects were assessed for thyroid morphology by thyroid ultrasonography.Vitamin D level was lower in hypothyroid patients than in control subjects. Vitamin D was also inversely related to TSH, HOMA-IR, and levels of anti-TG and anti-TPO. VDR polymorphism (Fok1 and Apa1) had no relation to TSH or vitamin D levels in both patients and control groups. Low vitamin D levels were associated with increased thyroid vascularity and nodularity; furthermore, vitamin D was inversely proportional to thyroid gland volume. Correlation of HOMA-IR with the levels of both anti-TG and anti-TPO in the 70 subjects proved that HOMA-IR was positively correlated to both antibodies.This study confirmed the association of vitamin D deficiency with hypothyroidism, thyroid autoimmunity, increased volume, nodularity, and vascularity of thyroid gland in hypothyroid patients as well as increased HOMA-IR. It proved the association between HOMA-IR and thyroid autoimmunity. The study proved no association between VDR polymorphisms (Fok1 and Apa1) with either vitamin D levels or TSH levels.