Hydroxyurea (HU) has been successfully used in patients with β-thalassemia intermedia (β-TI). We aimed to evaluate the effect of the long-term use of HU on thyroid function in patients with β-TI. Seventy-five patients with β-TI aged≥11 years and taking HU were randomly selected during 2010 in southern Iran. Thirty-one patients with β-TI without HU were considered as a control group. Serum levels of thyroid stimulating hormone (TSH) and T4 were measured. The mean age of the participants was 22.7±5.1 years (age range=12-41 years). Serum ferritin level had no significant correlation with HU consumption (P>0.05). Overall, we detected 10 (9.4%) patients with hypothyroidism. We found that the use of HU at a dose of 8-15 mg/kg/day has no significant association with thyroid function in β-TI patients. However, due to the small sample size in our study, documentation of this finding needs further studies with higher numbers of patients.