This paper deals with a methodology for calculating the greenhouse gas (GHG) balances of bioenergy systems producing electricity, heat and transportation biofuels from biomass residues or crops. Proceeding from the standard Life-Cycle Assessment (LCA) as defined by ISO 14040 norms, this work provides an overview of the application of the LCA methodology to bioenergy systems in order to estimate GHG balances. In this paper, key steps in the bioenergy chain are identified and the bioenergy systems are compared with fossil reference systems producing the same amount of final products/services. The GHG emission balances of the two systems can thus be compared. Afterwards, the most important methodological assumptions (e.g. functional unit, allocation, reference system, system boundaries) and key aspects affecting the final outcomes are discussed. These key aspects are: changes in organic carbon pools, land-use change effects (both direct and indirect), N(2)O and CH(4) emissions from agricultural soils and effects of crop residue removal for bioenergy use. This paper finally provides some guidelines concerning the compilation of GHG balances of bioenergy systems, with recommendations and indications on how to show final results, address the key methodological issues and give homogenous findings (in order to enhance the comparison across case studies). (C) 2009 Elsevier Ltd. All rights reserved.