A model laboratory scale membrane bioreactor (MBR) for the treatment of swine wastewater has been studied to illustrate the removal mechanisms of selected endocrine disrupting compounds (EDCs). A pilot scale MBR was also operated to confirm the results from the laboratory scale study. Liquid extraction with cyclohexane followed by yeast estrogen screen (YES) assay was used to determine the estrogenic activity (EA) of wastewater and sludge samples. Both laboratory and pilot scale MBRs were demonstrated to be effective systems for EA removal from swine wastewater. The average removal rate was 93.5% in terms of EA in the soluble phase of swine wastewater, and 94.5% in terms of total EA. During the steady-state operation period total COD removal efficiencies ranged from 68.5% to 82.7% and up to 99.9% removal of NH3-N was achieved with proper pH control. A model mass balance revealed that over 85% of the influent EA was reduced through MBR process by degradation or evaporation. An average of 9.4% of the influent EA was removed from the MBR system in the wasted sludge, whereas 5.4% of the EA in the influent was found in the treated effluent.