Objective: To determine the prevalence of thyroid autoantibodies and the associated factors in euthyroid subjects. Methods: 300 euthyroid subjects, chosen by stratified sampling from an inception cohort of 1335 individuals, were included. Thyroid function was evaluated by measuring the serum levels of TSH (0.3–4.5 μIU/mL) and FT4 (5.2–12.7μg/dL). Anti-peroxidase (TPOAbs), anti-thyroglobulin (TgAbs), and anti-TSH receptor (TrAbs) antibodies were evaluated with 23 additional autoantibodies as well as vitamin D (VitD) levels. The analysis included sociodemographic, clinical, and environmental characteristics. Data were analyzed by bivariate and multivariate tests. Results: Thyroid autoimmunity was observed in 15.3% of the subjects (TPOAbs 11.3% and TgAbs 2.0%). In six individuals, both autoantibodies were positive. TrAbs were not detected in any individual. Familial thyroid disease (β = 3.4, 95% CI: 1.2–9.5, P = 0.021), the presence of other autoimmune diseases (β = 10.8, 95% CI: 1.6–72.9, P = 0.014) VitD insufficiency (P = 0.030), never smoke (β = 6.9, 95% CI: 1.6–30.4, P = 0.010), drinking more than 4 cups of coffee (β = 3.8, 95% CI: 1.1–13.1, P = 0.036), and a higher number of years exposed to wood smoke (P = 0.04) were associated with thyroid autoimmunity. In the case of TPOAbs, familial thyroid disease (β = 4.9, 95% CI: 1.7–14.0, P = 0.003), never smoke (β = 5.7, 95% CI: 1.4–21.0, P = 0.002), and drinking more than 4 cups of coffee (β = 3.6, 95% CI: 1.1–13.1, P = 0.047) were associated with their positivity. In addition, the presence of anti–SS–A/Ro52 (β = 36.7, 95% CI: 2.5–549.9, P = 0.009) and anti-Ku antibodies (β = 10.2, 95% CI: 1.1–100.7, P = 0.046) was also associated with TPOAbs. The presence of African ancestry (β = 10.5, 95% CI: 1.7–63.2, P = 0.01), anti–SS–A/Ro52 (β = 15.8, 95% CI: 1.2–198.6, P = 0.03), and anti-CENP-B antibodies (β = 31.2, 95% CI: 1.8–565.9 P = 0.02) were associated with TgAbs. Conclusion: Latent thyroid autoimmunity is not rare. Environmental, genetic, and immunological factors as well as ancestry are associated risk factors. These results would facilitate the implementation of screening strategies in order to provide timely diagnosis and treatment.