According to the existing EU regulation co-existence between genetically modified, conventional and organically grown plants is the general principle in EU agriculture. The paper analyses the effects of this regulation in a landscape in Southern Germany which is characterized by small-scaled fields. Using GIS simulation experiments it could be shown that a substantial proportion of fields which are cultivated with non-GM varieties will be influenced by cross pollination of Bt maize in two model regions. This effect also results in economic losses or additional costs for farmers operating in these regions. Altogether, there is need for clear and easy-to-handle implementation of co-existence schemes in particular in such small-scale farming regions like Bavaria.