Central nervous system (CNS) dysfunction is an important consequence of thyroid deficiency. Cranial nerves are frequently affected in hypothyroid process. On routine nerve conduction studies, symptomatic peripheral and cranial neuropathy can be detected, however, diagnosing subclinical cranial neuropathy pose the major problem. Blink reflex (BR), has been shown to be an effective method for revealing subclinical involvement of cranial nerves in generalized neuropathies. The present study was undertaken to evaluate the efficacy of BR as a method for early diagnosis of subclinical cranial neuropathy in hypothyroid patients with or without overt peripheral polyneuropathy. A case control study was conducted on 150 subjects aged 18 years and above (100 controls, 50 cases). A routine nerve conduction study and BR evaluation was done in all the subjects. We found abnormal BR response in 50% of hypothyroid patients studied. In hypothyroid patient without polyneuropathy R1 latency was significantly prolonged (P<0.05 Vs control).Ipsilateral and contralateral R2 latencies were significantly prolonged in hypothyroid cases with or without polyneuropathy on bilateral stimulation. Magnitude of prolongation was greater in with polyneuropathy group. In conclusion, study suggests that BR is a useful non-invasive method for the detection of clinically silent cranial nerve compromise in hypothyroid patients