Organic matter exposed to microwave radiation triggers standard thermal effects as well as a range of so called non-thermal effects. The present work examined the non-thermal effects of microwave radiation on the biofilm in bioreactors with immobilised biomass. Microwave-exposed and conventionally heated reactors were used and both groups of reactors operated on analogous technological parameters. The analysis of the treated sewage demonstrated a significant increase in nitrification and denitrification efficiency in the bioreactors treated with microwave radiation. An analysis of bacteria diversity based on DGGE method showed significantly different bacterial communities developed in the reactors exposed to the microwave radiation in comparison to the control reactors. Moreover, bacterial richness measured by Shannon index was significantly higher in the microwave treated samples (Mann-Whitney's test, p < 0.05). These findings indicate that microwave radiation can affect the structure and function of bacterial communities independent of thermal effects. (c) 2007 Elsevier Ltd. All rights reserved.