The degradation of three estrogens, two endocrine disruptors and ten pharmaceutical substances in a membrane separation bioreactor was experimentally examined. Higher removal of acidic pharmaceutical substances was obtained in the case of lower pH operation because of the increased tendency of adsorption to the sludge particles. The target substances attached to the sludge were not accumulated in the reactor and they were biologically degraded. The membrane used in this study was a microfiltration membrane which has much larger pores than target substances. However, the permeate concentration was lower than the water phase concentration in the reactor probably due to activated sludge deposition onto the membrane surface. The additional removal by the membrane was increased with the time elapsed, though the removal was not significantly high for the relatively hydrophilic compounds.