The possible use of Genetically Modified (GM) plants in future agriculture needs in-depth investigations of ecological and economic consequences. The investigations are important for both the European Commision (EC), who needs specifications of how to do the GM risk assessment, and to farmers and the public who are concerned about the possible ecological implications. The ECOGEN (www.ecogen.dk) project Soil ecological and economic evaluation of genetically modified crops is an EU-funded project aimed at combining simple lab tests, multi-species model ecosystems and field studies to acquire mechanistic and realistic knowledge about economic and ecological impacts of GM crops on the soil (Cortet et al, 2005, Griffiths et al, 2005, Vercesi et al, 2005). Economic trade-offs are assessed and related to ecological effects (Scatasta at al, 2005). One of the goals of the project is to develop a computer-based decision support system for the assessment of economic and ecological impacts of using GM crops, with special emphasis on soil biology and ecology. For model development, we have taken the approach of qualitative multi-attribute modeling (Bohanec 2003). The idea is to develop a hierarchical model, consisting of qualitative attributes and utility (aggregation) functions, represented by decision rules. The development is supported by the software tool DEXi, which facilitates the development of a tree of attributes, definition of aggregation rules, evaluation of options (cropping systems in this case), what-if analysis and charting. Using this approach, we developed a model for the assessment of the impact of GM and non-GM cropping systems to soil quality. In this paper, we describe the model and its application to the assessment of impacts to soil of using conventional and Bt maize to three fields in France and Denmark. The model is hierarchical, consisting of 37 attributes in total, grouped into 7 hierarchical levels. There are 24 input attributes, most of which measure the richness and biomass of representative soil organisms. The assessment of soil quality is based on two main indicators: (1) soil diversity (assessed through microfauna, mesofauna and macrofauna richness) and (2) soil functioning (in terms of leaching, comminution, mineralisation and plant growth).