Yeast estrogen screen (YES) bioassay and liquid chromatography-mass spectrum-mass spectrum (LC-MS-MS) analysis were performed to investigate the fate of active and potential endocrine disrupting compounds in 3 pilot-scale and 2 lab-scale membrane bioreactor (MBR) systems. Compared with the overall estrogenicities of sewage treatment plant (STP) effluents from references, the MBR systems studied have relatively good performance in the removal of estrogenicity. Estrone (E1) was removed with relatively high efficiency (80.2-91.4%), but 17beta-estradiol (E2) was removed with moderate efficiency (49.3-66.5%) by the MBRs. However, the experimental results indicated that after the treatment by MBR, substantial amounts of E1, estrone-3-sulfate (E1-3S), estrone-3-glucuronide (E1-3G), and 17beta-estradiol-glucuronides (E2-G) passed through treatment systems and entered into the aquatic environment. The reduction in the levels of overall equivalent E1 (68.4%) and that of overall equivalent E2 (80.8%) was demonstrated for the pilot-scale MBR-B. For alkylphenol compounds, bisphenol A (BPA) was removed well with a removal efficiency of 68.9 -90.1%, but 4-nonylphenol (4-NP) concentration was amplified (removal efficiency of -439.5 to -161.1%) after MBR treatment which could be caused by the transformation of its parent compounds, nonylphenol polyethoxylates (NPnEOs). The amounts of adsorbed estrogens per kg dry mass was relatively low, due to short hydraulic retention time and high mixed liquor suspended solids in MBRs, compared to that in STPs.