In this paper, which was prepared as part of IEA Bioenergy Task XV (“Greenhouse Gas Balances of Bioenergy Systems”), we outline a standard methodology for comparing the greenhouse gas balances of bioenergy systems with those of fossil energy systems. Emphasis is on a careful definition of system boundaries. The following issues are dealt with in detail: time interval analysed and changes of carbon stocks; reference energy systems; energy inputs required to produce, process and transport fuels; mass and energy losses along the entire fuel chain; energy embodied in facility infrastructure; distribution systems; cogeneration systems; by-products; waste wood and other biomass waste for energy; reference land use; and other environmental issues. For each of these areas recommendations are given on how analyses of greenhouse gas balances should be performed. In some cases we also point out alternative ways of doing the greenhouse gas accounting. Finally, the paper gives some recommendations on how bioenergy systems should be optimized from a greenhouse-gas-emissions point of view.