Objective: Alopecia areata is commonly associated with autoimmune disorders such as thyroid dysfunction. This paper aims to evaluate thyroid dysfunction in alopecia areata patients among the Iranian population. Material and Methods: In this case-control study, 80 alopecia areata patients were recruited along with 122 age and sex-matched healthy subjects; serum thyroid stimulating hormone and anti-thyroid peroxidase levels were then compared between the groups. Results: All alopecia areata patients had similar rate of increased thyroid stimulating hormone (10% vs. 8.2%, p=0.66) and anti-tiroid peroksidaz levels (15.6% vs. 23.8%, p=0.14) as compared to the controls. Patients with disease duration >6 months had significantly higher anti-tiroid peroksidaz levels (42.9% vs. 16.9%, p=0.01), with no difference in thyroid stimulating hormone levels (19% vs. 6.8%, p=0.1). Female patients also had higher abnormal anti-tiroid peroksidaz levels (35% vs. 12.5%, p=0.01) compared to the males. Conclusion: Thyroid stimulating hormone and thyroid antibodies are not significantly increased in alopecia areata patients when compared to the normal population. Thyroid antibodies, however, were found to be increased in females and with the progression of disease duration. Therefore, thyroid function and antibodies must be evaluated in alopecia areata patients, especially in females, and along different time periods in individuals having the disease for a long time.