Background Autoimmune disease (AID) patients always present with increased risk of psychiatric disorders, and thyroid function or thyroid hormone may play a critical role in the development of anxiety and depression. Thus, this study aimed to assess the free triiodothyronine (FT3), free tetraiodothyronine (FT4), thyroid‐stimulating hormone (TSH) levels, and their correlations with anxiety/depression in patients with AID. Methods Ninety‐eight AID patients and 100 health controls (HCs) were recruited. Serum samples were obtained from all the participants to detect FT3, FT4, and TSH levels. Anxiety and depression were determined using the HADS assessment. Results HADS‐Anxiety score, anxiety subject percentage, HADS‐Depression score, and depression subject proportion were elevated in AID patients compared with HCs. FT3 and FT4 were downregulated while TSH was upregulated in AID patients compared with HCs. In AID patients, FT3 and FT4 negatively correlated with HADS‐Anxiety score, and they were downregulated in patients with anxiety compared to patients without anxiety. Meanwhile, FT3 and FT4 were negatively associated while TSH level positively associated with HADS‐Depression score. Besides, FT3 and FT4 reduced, but TSH level was of no difference in patients with depression compared to patients without depression. Additionally, increased FT4 independently correlated with both reduced anxiety risk and depression risk. Conclusions FT3, FT4, and TSH are dysregulated, and FT4 has the potential to serve as an independent biomarker related to anxiety as well as depression in AID patients. These findings may provide some information on the values of thyroid hormones in facilitating the management of AID patients with anxiety/depression.

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