In 1994, Madoni created the Sludge Biotic Index (SBI) based on the presence and abundance of certain key protozoan groups. The use of this index has become increasingly common in wastewater treatment plant control and its applicability has been demonstrated. In this study, we applied the SBI index to a pilot-scale membrane bioreactor equipped with polyvinylidenefluoride hollow fibre membranes (0.04 mu m pore size). Two different sludge retention times (SRT) - 25 and 35 days -were assayed, with a constant hydraulic retention time of 30 h. Operational conditions for MBR cause the fragmentation of flocs which are broken down into small dissipated elements with abundant dispersed bacteria. This process determines protozoan composition and colonization of the activated sludge. Results of the experiment showed a constant predominance of small flagellates, carnivorous ciliated protozoa and rotifers, above all in assays with 35-day SRT, independently of effluent quality. However, continuous changes in microbiota were observed, with a clear tendency for the SBI to increase over time as the sludge became more stable. Therefore, although it was not possible to establish an association between SBI and effluent quality for MBR activated sludge, the stabilisation of the process may be related to SBI. (C) 2009 Elsevier B.V. All rights reserved.