Mercury (Hg) has been implicated as an immunotoxicant in experimental animal models, but its role in the induction of human autoimmunity remains unclear due to contradictory findings. Therefore, it has been claimed that it is important to examine other populations in order to clarify the role of Hg in these diseases. The aim of this study was to investigate whether occupational Hg exposure due to artisanal gold mining is associated with the prevalence of autoimmune biomarkers. A cross-sectional study was conducted comparing Hg-exposed gold miners (n = 164) with a control population (n = 127). Hair, blood, and 24-h urine samples were collected for measures of Hg levels, as well as of anti-nuclear antibodies (ANA) and rheumatoid factor (RF). Participants were clinically evaluated by a general practice physician, a rheumatologist, and a toxicologist. Statistically significant differences (p < 0.001) were found between Hg-exposed and non-exposed groups for all Hg biomarkers tested: blood (7.03 versus 2.46 µg Hg/L), urine (3.96 versus 1.48 µg Hg/g creatinine), and hair (0.79 versus 0.39 µg Hg/g). No difference was observed in ANA (cut-off titre of 1:80; PR = 0.93, 95% CI = 0.45-1.90) and RF (cut-off = 30 IU/mL; PR = 0.062, 95% CI = 0.03-1.08) status between the groups. In conclusion, the findings here do not support the hypothesis that Hg exposure due to artisanal gold mining activities had a significant impact on autoantibodies as biomarkers of autoimmune diseases. In a review context, the epidemiological findings were interpreted in light of the conflicting data in the literature about how Hg exposure was linked to development of autoantibodies. Validation of these findings in prospective studies is needed to firmly establish the role of Hg in development of autoimmunity in human populations.