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Abstract Background Data regarding the relation between both subclinical thyroid dysfunction, thyroid autoantibodies and clinical outcomes in stroke patients are limited. This study aimed to evaluate subclinical thyroid dysfunction and thyroid autoantibodies production in acute stroke patients and their relation to long term stroke outcome. We recruited 138 patients who were subjected to thorough general, neurological examination and brain imaging. Blood samples were collected for measurement of levels of serum thyroid function [free tri-iodothyronine (FT3), free thyroxin (FT4), thyroid stimulating hormone (TSH)], thyroid autoantibodies within 48 h after hospital admission. FT4 and TSH after 1 year were done. The stroke severity was assessed at admission by the National Institutes of Health Stroke Scale (NIHSS). The stroke outcome was assessed at 3 months and after 1 year by the modified Rankin Scale (mRS). We divided the patients into two groups according to thyroid autoantibodies (positive and negative groups). Results Subclinical hyperthyroidism was found in 23% of patients, and subclinical hypothyroidism in 10% of patients. Euthyroidism was detected in 67% of patients. 34% patients had positive thyroid autoantibody. Positive thyroid autoantibodies were commonly found in those with subclinical hyperthyroidism (28%), followed by subclinical hypothyroidism (21%) and euthyroidism (14%). 73% and 59% of stroke patients had poor outcomes (mRS was > 2) at 3 months and 1 year respectively with no significant difference between ischemic and hemorrhagic stroke patients. In the positive group final TSH level, NIHSS score at admission, and disability at 1 year were significantly higher compared with the negative group. Poor outcome was significantly associated with higher NIHSS score at admission, positive thyroid autoantibodies, subclinical hyperthyroidism, and atrial fibrillation. Conclusions Subclinical thyroid dysfunction could be found in stroke patients with positive thyroid autoantibodies. Subclinical hyperthyroidism and thyroid autoantibodies were associated with a poor outcome at 1 year in first-ever acute stroke patients especially in those presented with atrial fibrillation and higher NIHSS score at admission.