Biological systems for the treatment of wastewater have to provide optimum sludge retention to achieve high removal efficiencies. In the case of slow-growing micro-organisms, such as anaerobic ammonia-oxidizing (Anammox) bacteria, episodes of flotation involving biomass wash-out are especially critical. In this study a strategy based on the introduction of a mix period in the operational cycle of the Anammox Sequencing Batch Reactor (SBR) was tested for its effects on biomass retention and nitrite removal. Using this new cycle distribution the biomass retention inside the reactor improved as the solids concentration in the effluent of the SBR decreased from 20-45 to 5-10 mg VSS dm(-3) and the biomass concentration inside the reactor increased from 1.30 to 2.53 g VSS dm(-3) in a period of 25 days. A decrease of the sludge volume index (SVI) from 108 to 60 cm(3) g VSS-1 was also observed. Complete depletion of nitrite was achieved in the reactor only with the new cycle distribution treating nitrogen loading rates (g N-NO2- + g N-NH4+ dm(-3) d(-1)) up to 0.60 g N dm(-3) d(-1). (C) 2004 Society of Chemical Industry.