The work presents the possibility of elimination of Clostridium perfringens in surplus activated sludge handling by microwave radiation. An assessment of the impact of microwave radiation as a disintegration and higienisation method of surplus activated sludge was based on an analysis of the value of COD and changes in population of the bacteria Clostridium perfringens and overall sticks in the family Enterobacteriaceae. Basis on the results of the research was concluded that microwave radiation (700W and 900W) shows disintegration action expressed in COD value in the supernatant increase: 12 times increase value of COD with power 700W and 13 times for 900W radiation power. Electromagnetic wave contributed to partial higienisation of surplus activated sludge. The number of Clostridium perfringens decrease about 52% and 56% during the 120s of higienisation process with power 700W and 900W, respectively. Reduction of the overall number of bacteria under the influence of microwave radiation was 42% and 51% (respectively for 700W and 900W), and sticks from the family Enterobacteriaceae from 54% to 70% depending on the power of radiation, the time of operation and biochemical properties.