This large-scale study aims to analyze the association of systemic lupus erythematosus (SLE) with thyroid diseases. Methods: In this retrospective, nationwide cohort study, 1633 newly diagnosed SLE patients from the National Health Insurance Research Database in 2000 were examined and data on patients with diagnoses of hyperthyroidism, hypothyroidism, and autoimmune thyroiditis were collected from 2000 to 2009. We subdivided these SLE patients by the presence of overlap syndrome. Comparison

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... 6532 age-and sex-matched controls was performed. Results: The cumulative incidence of thyroid disease in SLE patients was lower than in controls (8.1% vs. 16.9%, p < 0.001). Among SLE patients, 39.7% had overlap syndrome. The overlap syndrome group had a higher cumulative incidence of thyroid diseases (10.96% vs. 4.57%, p < 0.0001), hypothyroidism (3.86% vs. 1.93%, p Z 0.017), and autoimmune thyroiditis (4.63% vs. 0.71%, p < 0.0001) than SLE patients without overlap syndrome. Comparing the data with the non-SLE-matched control group by logistic regression model revealed a decreased risk of thyroid diseases with odds ratios (ORs) of 0.25 and 0.62 [95% confidence interval (CI) 0.18 e0.33, 0.48e0.80], and hyperthyroidism with ORs of 0.21 and 0.30 (95% CI 0.14e0.31, 0.20 e0.45) in SLE patients without and with overlap syndrome. SLE patients without overlap syndrome had a lower risk of hypothyroidism with an OR of 0.53 (95% CI 0.53e0.86) and autoimmune thyroiditis with an OR of 0.26 (95% CI 0.12e0.56). SLE patients with overlap syndrome showed a similar risk of hypothyroidism with an OR of 0.92 (95% CI 0.66e1.53) and a higher risk of autoimmune thyroiditis with OR of 1.69 (95% CI 1.14e2.51). Journal of Microbiology, Immunology and Infection (2015) 48, 676e683 Conclusion: SLE patients had a significantly lower rate of thyroid diseases and hyperthyroidism than matched controls. Among SLE patients, risks of hypothyroidism and autoimmune thyroiditis were different in the presence of overlap syndrome. This finding is novel and important for clinical practices.