This Scientific and Technical Report (STR) describes the main reasons for the growth of the different filamentous microorganisms in activated sludge, and the biological molecular tools today available for the identification of the main biomass components. The wide range of experiences around the world is documented and the methods to avoid the proliferation of these organisms are presented and critically reviewed in this IWA STR. This will be a valuable source of information for all those concerned with activated sludge separation including both plant operators and academic researchers.