AIM: The aim of the present study was to evaluate the usefulness of the blink reflex as a method for obtaining an early diagnosis of central nervous system dysfunction in hypothyroid patients who do not have signs or symptoms of nervous system dysfunction. MATERIALS AND METHODS: Forty-two patients (3 males, 39 females), mean age 40 (±11), with newly diagnosed primary hypothyroidism and 30 healthy control subjects were included in the study. In all patients, the cause of hypothyroidism was chronic autoimmune thyroiditis. For blink reflex testing, subjects lay supine on a bed in a warm room with eyes gently closed. Recordings were performed with an EMG machine (Nihon Kohden/Neuropack), with a filter setting of 20 Hz to 10 kHz, using an analysis time of 50 ms. Recordings were performed with surface recording electrodes (Dantec 13K60, Copenhagen, Denmark). RESULTS: Second ipsilateral response (R2Y) and second contralateral response (R2C) latencies in hypothyroidism were prolonged relative to controls, and the differences were statistically significant (P < 0.001 and P < 0.001, respectively). Latency of R1, R2Y, and R2C did not correlate with free T3, free T4, or TSH values in the hypothyroid group. CONCLUSION: The finding of abnormal blink reflex responses in hypothyroid individuals raises the notion that they may be useful in detecting early changes and in the follow-up of the patients with the disorder. © 2007 Lippincott Williams & Wilkins, Inc.