The objectives of this study were to evaluate whether there were higher rates of primary congenital hypothyroidism (PCH) or elevated concentrations of thyroid-stimulating hormone (TSH) in a community where perchlorate was detected in groundwater wells. The adjusted PCH prevalence ratio and 95% confidence interval (CI) comparing the study community to San Bernardino and Riverside counties combined was 0.45 (95% CI=0.06-1.64). The odds ratios for elevated TSH concentration were 1.24 (95% CI=0.89-1.68) among all newborns screened and 0.69 (95% CI=0.27-1.45) for newborns whose age at screening was 18 hours or greater. Age of the newborn at time of screening was the most important predictor of the TSH level. These findings suggest that residence in a community with potential perchlorate exposure has not impacted PCH rates or newborn thyroid function.