The purpose of this study was to determine the effects of perchlorate on thyroid function in mosquitofish. Adult mosquitofish were exposed to 0, 0.1, 1, 10, 100, and 1000 mg/L sodium perchlorate for 2, 10, and 30 d. Whole body thyroxin (T4) content and histological assessment of thyroid follicles (e.g., follicular epithelial height, hyperplasia, hypertrophy, and colloid depletion) were used to gauge alterations in thyroid function. Follicular epithelial cell height, hyperplasia, and hypertrophy increased with increasing perchlorate concentration, especially in fish exposed for 30 d, and these effects were statistically significantly different from control at concentrations as low as 0.1 mg/L (nominal concentration). The percent occurrence of follicles with depleted colloid decreased with increasing perchlorate concentration, which is contrary to what is expected with thyroid inhibition. There also was a decrease in whole body T4 concentration in fish exposed to perchlorate for 30 d, but clear dose-response relationships were less evident for whole body T4 than for histopathological endpoints. In conclusion, thyroid histopathology provides a sensitive biomarker for thyroid endocrine disruption at environmentally relevant concentrations of sodium perchlorate, and whole body T4 is a less sensitive indicator of perchlorate exposure than is histopathology.