Background and Objective: Hypothyroidism is a known consequence of the external beam radiotherapy to the neck encompassing the thyroid gland for over 40 years. The aim of this study was to find out the incidence of hypothyroidism in patients with head and neck cancer treated with radiotherapy, when radiation portals included whole of the thyroid gland. Materials and Methods: This prospective non-randomized study was conducted from December 2004 to February 2006. In this regard, 39 patients with head and neck malignancies referred to radiation oncology center of Hamedan whom treated with the external beam radiotherapy, whose radiation portals included the whole of the thyroid gland. Thyroid function tests were done at the beginning of treatment, one month, three months, six months, and one year after the completion of radiotherapy. Results: Out of 39 patients, two were excluded from the study as they had history of hypothyroid before the initiation of treatment. The next two were excluded from data analysis because they did not undergo regular follow-up. Of the patients attending the follow-up clinic, 31% were found to have sub-clinical hypothyroidism (TSH>4.5 mU/l) during a year. Conclusion: Since a significant number of patients developed hypothyroidism following radiotherapy on the neck, thyroid function tests should be included in the routine follow-up protocol of such patients. Certain questions have emerged from this study, which need a large randomized study to find out the answers.