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Background: The effect of subclinical thyroid dysfunction on vascular atherosclerosis remains uncertain. The objective of this study was to elucidate the association between sustained subclinical thyroid dysfunction and carotid plaques, which are an early surrogate marker of systemic atherosclerosis. Methods: The study included 21,342 adults with consistent thyroid hormonal status on serial thyroid function tests (TFTs) and carotid artery duplex ultrasonography at a health screening center between 2007 and 2014. The effect of subclinical thyroid dysfunction on baseline carotid plaques and newly developed carotid plaques during 5-year follow-up was determined by logistic regression analyses and GEE (Generalized Estimating Equations), respectively. Results: Carotid plaques were more common in the subclinical hypothyroidism (55.6%) than the euthyroidism (47.8%) at baseline. However, in multivariable analysis, thyroid status was not a significant risk for the carotid plaques at baseline. Instead, traditional cardiovascular risk factors, such as age (P <0.001), systolic blood pressure (P = 0.023), fasting blood glucose (P = 0.030), and creatinine (P = 0.012) were associated with baseline carotid plaques in subclinical hypothyroidism. In longitudinal analyses of subjects who were followed up for more than 5 years, there was no significant difference in the cumulative incidence of new carotid plaques according to time between subjects with subclinical hypothyroidism and those with euthyroidism (P = 0.392). Conclusions: Sustained subclinical thyroid dysfunction did not affect the baseline or development of carotid plaques in healthy individuals. [ABSTRACT FROM AUTHOR]