Findings from national surveys suggest that everyone in the US is exposed to perchlorate. At high doses, perchlorate, thiocyanate, and nitrate inhibit iodide uptake into the thyroid and decrease thyroid hormone production. Small changes in thyroid hormones during pregnancy, including changes within normal reference ranges, have been linked to cognitive function declines in the offspring. To evaluate the potential effects of low environmental exposures to perchlorate on thyroid function. Serum thyroid hormones and anti-thyroid antibodies and urinary perchlorate, thiocyanate, nitrate, and iodide concentrations were measured in 1,880 pregnant women from San Diego County during 2000-3, a period when much of the area’s water supply was contaminated from an industrial plant with perchlorate at levels near the 2007 California regulatory standard of 6 ?g/L. Linear regression was used to evaluate associations between urinary perchlorate and serum thyroid hormone concentrations in models adjusted for urinary creatinine and thiocyanate, maternal age and education, ethnicity, and gestational age at serum collection. The median urinary perchlorate concentration was 6.5 ?g/L, about 2-times higher than in the general US population. Adjusted associations were identified between increasing log10 perchlorate and decreasing total thyroxine (T4) (regression coefficient (B)=-0.70; 95% confidence interval (CI), -1.06, -0.34), decreasing free thyroxine (fT4) (B=-0.053; 95% CI, -0.092, -0.013), and increasing log10 thyroid stimulating hormone (B=0.071; 95% CI, 0.008, 0.133). These results suggest that environmental perchlorate exposures may impact thyroid hormone production during pregnancy. This could have implications for public health given widespread perchlorate exposure and the importance of thyroid hormone in fetal neurodevelopment.