This paper presents a comparative energy system analysis of different technologies utilising organic waste for heat and power production as well as fuel for transport. Technologies included in the analysis are second-generation biofuel production, gasification, fermentation (biogas production) and improved incineration. It is argued that energy technologies should be assessed together with the energy systems of which they form part and influence. The energy system analysis is performed by use of the EnergyPLAN model, which simulates the Danish energy system hour by hour. The analysis shows that most fossil fuel is saved by gasifying the organic waste and using the syngas for combined heat and power production. On the other hand, least greenhouse gases are emitted if biogas is produced from organic waste and used for combined heat and power production; assuming that the use of organic waste for biogas production facilitates the use of manure for biogas production. The technology which provides the cheapest CO2 reduction is gasification of waste with the subsequent conversion of gas into transport fuel.