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Background: Benzodiazepines are widely used as psychoactive agents and the side effects of benzodiazepines to the endocrine system are reported. Objective: This study was designed to explore the effects of the benzodiazepines - lorazepam and clonazepam - on thyroglobulin (Tg), anti-thyroglobulin (aTg), anti-thyroid peroxidase (aTPO), and thyroid stimulating hormone (TSH). Materials and Methods: Eighteen male Wistar rats were randomly divided into three groups: control (C), lorazepam-treated, and clonazepam-treated groups. The changes in Tg, aTg, aTPO, and TSH in these three groups were compared after 4 weeks. Results: The levels of Tg and aTg in the lorazepam-treated and clonazepam-treated rats significantly increased compared to the control group. But there was no significant difference in the levels of TSH and aTPO between lorazepam-treated and clonazepam-treated rats in comparison with the control group rats. Conclusion: The thyroid gland is affected by lorazepam and clonazepam, which are used in epilepsy, bruxism, anxiety, insomnia, and other psychic disorders.