Thermal treatment of waste represents an integral part of well-developed waste management systems worldwide. About 85.8 Mt of waste were treated with energy recovery and about 42.7 Mt were incinerated without energy recovery in 27 EU states in 2010. Up-to-date waste-to-energy (WtE) plants dispose waste and produce heat and/or electricity at the same time with minimal negative impact on the environment. Therefore complex flue gas cleaning systems are implemented to comply with strict environmental limits set on gaseous products of combustion process. Operation of these sophisticated systems is associated with additional energy consumption, and significant adverse effects to the whole WtE technology performance in terms of energy. Simulation model of WtE plant with annual capacity of 100 kt of municipal solid waste was created. In-house developed software W2E (Waste-to-Energy) was used for this purpose as well as for subsequent simulation addressing overall heat-and-mass balance calculation. Internal material and energy flows associated with application of different flue gas cleaning systems were analysed. The relation between performance in terms of energy efficiency and harmful compound removal efficiency was discussed.