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Background:Thyroid autoimmunity was thought to be rare in Africans but there is evidence that its prevalence is increasing. Since undetected autoimmune thyroid disease carries considerable morbidity, this study set out to determine the proportion of patients with goitre who have thyroid autoantibodies and the relationship, if any, between the presence of thyroid autoantibodies, thyroid function and thyroid size.Methods:The study was cross-sectional and conducted over a 12-month period. It involved 100 subjects with goitre and 50 apparently healthy controls without goitre, matched for age and sex. Thyroid dysfunction was assessed by history, clinical examination and biochemical tests, thyroid peroxidase and thyroglobulin antibodies. The size of the thyroid gland was assessed by ultrasound.Results:Fifty-seven percent (57%) of study subjects were euthyroid, 38% were hyperthyroid, while 2% were hypothyroid. The overall prevalence of elevated thyroid peroxidase antibody (TPOAb) in the subjects with goitre was 35% and 8% in the controls (p < 0.001). Elevated thyroglobulin antibody (TgAb) was found in 24% of subjects with goitre and 12% of controls (p = 0.083). Elevated TPOAb was found in 76.3% of subjects who were hyperthyroid, 7% of subjects who were euthyroid and 100% of subjects who were hypothyroid (p < 0.001). Elevated TgAb level was present in 36.8%, 15.8% and 50% of subjects with hyperthyroid, euthyroid and hypothyroid goitre respectively (p = 0.068). A positive correlation was observed between TPOAb and erythrocyte sedimentation rate (r = 0.582, p < 0.001) and TgAb and erythrocyte sedimentation rate (r = 0.176, p = 0.08). The correlation between TPOAb and thyroid volume (r = –0.139, p = 0.167) and that of TgAb and thyroid volume (r = –0.119, p = 0.238) was not significant.Conclusion:The prevalence of thyroid autoantibodies in patients with goitre is high in Nigeria. Thyroid peroxidase antibody is more prevalent than thyroglobulin antibody in thyroid disorders and appears to be a better marker than thyroglobulin antibody in detecting autoimmune thyroid dysfunction.