The fate of two differently labelled radioactive forms of 17alpha-ethinylestradiol (EE2) was studied during the membrane bioreactor (MBR) process. The laboratory-scale MBR specially designed for studies with radioactive compounds was operated using a synthetic wastewater representative of the pharmaceutical industry and the activated sludge was obtained from a large-scale MBR treating pharmaceutical wastewater. By applying in MBR a concentration of 8 g/L mixed liquor solid suspension and a sludge retention time of 25 days over the whole test period (35 days), the removal performance of C-, N- and P-ranged between 80% and 95%. Balancing of radioactivity could demonstrate that real mineralization is <1%, while radioactivity mainly remained sorbed in the reactor, resulting in a removal of approximately 80%. The same metabolite pattern in the radiochromatograms for the two different labelling protocols led us to assume that the elimination pathway does not involve the removal of the ethinyl group from EE2 molecule.