thyroid hormones in serum and in brain were measured in fetal and neonatal rat cortex after graded levels of a thyroid hormone synthesis inhibitor were administered to pregnant rat dams. A number of gene targets were assessed to look for measures of thyroid hormone action in these same tissues. This dataset is associated with the following publication: OShaughnessy, K., C. Wood, R. Ford, P. Kosian, M. Hotchkiss, S. Degitz, and M. Gilbert. Thyroid hormone disruption in the fetal and neonatal rat: Predictive hormone measures and bioindicators of hormone action in the developing cortex- ToxSci. TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, 163-179, (2018).