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It is generally known that there are many endocrine disrupting compounds (EDCs) in the effluents from wastewater treatment plants (WWTPs). Most research has focused on the occurrence of estrogenic or androgenic activities, while ignoring that there are environmental chemicals disrupting thyroid system, which is essential for growth and development in both humans and animals. In the present work, a two-hybrid yeast assay was conducted to evaluate the removal efficiencies of agonistic or antagonistic thyroid receptor (TR) mediated effects in different treatment processes of three WWTPs located in Beijing. We found no TR agonistic, but TR antagonistic activities in all processes from the WWTPs. The TR antagonistic activities in organic extracts of water samples were then calibrated regarding to a known TR-inhibitor, amiodarone hydrochloride (AH). The observed concentration of TR disrupting substances ranged from 2.35 × 10-8 to 6.19 × 10-7 mol/L AH in Gaobeidian WWTP, 3.76 × 10-s to 8.75 x 10-s mol/L AH in Lugouqiao WWTP,and 4.80 × 10-9 to 2.55 × 10-s mol/L AH in Beixiaohe WWTP. Of the three WWTPs, the removal rates were 92.7%, 42.2%, and 23.1% respectively. Industrial sewage may contain more TR disrupting substances compared with domestic sewage. The recipient waters were found to contain considerable concentrations of TR disrupting substances that may cause adverse effects on the exposed organisms.