Modeling of economic and ecological impacts of genetically modified crops is a demanding task. We present some models made for the purpose of the ECOGEN project “Soil ecological and economic evaluation of genetically modified crops”. 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 genetically modified crops, with special emphasis on soil biology and ecology. The decision support system is based on a rule-based model incorporating both economic and ecological criteria. In this paper we present an extension to previous results specifying further two sub-models assessing economic impacts of cropping systems at farm and regional level. Following a real option approach we show how both social and private costs and benefits, both at farm and regional level, can be classified in reversible and irreversible, and what irreversibility means for the size of the uncertainty associated to the adoption of agricultural innovations. All the qualitative models are developed using a qualitative multi-attribute modeling methodology, supported by the software tool DEXi.