BACKGROUND: Partial nitrification-Anammox is a combined promising advanced biological process for the removal of nitrogen from wastewater, which allows important savings in energy consumption, sludge production, and organic carbon. Granular biomass appears to be an interesting alternative to conventional activated sludge, mainly because of its better settling properties. This study deals with the experimental results of a comparison between a conventional and a granular sequencing batch reactor (SBR) for the partial nitrification of reject water. RESULTS: After some days of operation, 30 days in the conventional SBR (system A) and 100 days in the granular SBR (system B), partial nitrificationwas achieved. Granular sludge showed much better settling properties than suspended biomass, with values of sludge volumetric index (SVI(10)) of 130 mL g(-1) in system A and 38 mL g(-1) in system B. Consequently, the solids concentration within the granular reactor was three times higher than for the conventional system while the concentration of solids in the effluent was 10 times higher in the conventional SBR. Morphology, microstructure and microbial populations in both systems were also studied. CONCLUSION: A partial nitrification process was successfully achieved in both systems, obtaining an effluent with a NO(2)(-)-N/NH(4)(+)-N ratio near 1, suitable for a following Anammox process. Granular biomass, mostly formed by round particles, showed better settling properties, leading to better sludge-effluent separation as well as higher biomass retention in the reactor. The granulation process does not affect bacterial populations, since they were the same in both systems. (C) 2011 Society of Chemical Industry