The aim of this study was to provide an ex ante assessment of the sustainability of genetically modified (GM) crops under the agricultural conditions prevailing in Switzerland. The study addressed the gaps in our knowledge relating to (1) the agronomic risks/benefits in production systems under Swiss conditions (at field and rotation/orchard level), (2) the economic and socio-economic impacts associated with altered farming systems, and (3) the agro-ecological risks/benefits of GM crops (at field and rotation/orchard level). The study was based on an inventory of GM crops and traits which may be available in the next decade, and on realistic scenarios of novel agricultural practices associated with the use of GM crops in conventional, integrated, and organic farming systems in Switzerland. The technology impact assessment was conducted using an adapted version of the matrix for “comparative assessment of risks and benefits for novel agricultural systems” developed for the UK. Parameter settings were based on information from literature sources and expert workshops. In a tiered approach, sustainability criteria were defined, an inventory of potentially available, suitable GM crops was drawn up, and scenarios of baseline and novel farming systems with GM crops were developed and subsequently submitted to economic, socio-economic, and agro-ecological assessments. The project had several system boundaries, which influenced the outcomes. It was limited to the main agricultural crops used for food and feed production and focused on traits that are relevant at the field level and are likely to be commercially available within a decade from the start of the project. The study assumed that there would be no statutory restrictions on growing GM crops in all farming systems and that they would be eligible for direct payments in the same way as non-GM crops. Costs for co-existence measures were explicitly excluded and it was assumed that GM foods could be marketed in the same way as non-GM foods at equal farm gate prices. The following model GM crops were selected for this study: (1) GM maize varieties with herbicide tolerance (HT), and with resistance to the European corn borer (Ostrinia nubilalis) and the corn rootworm (Diabrotica virgifera); (2) HT wheat; (3) GM potato varieties with resistance to late blight (Phytophthora infestans), to the nematode Globodera spp., and to the Colorado beetle (Leptinotarsa decemlineata); (4) HT sugar beet with resistance to “rhizomania” (beet necrotic yellow vein virus; BNYVV); (5) apples with traditionally bred or GM resistance to scab (Venturia inaequalis), and GM apples with stacked resistance to scab and fire blight (Erwinia amylovora). Scenarios for arable rotations and apple orchards were developed on the basis of the model crops selected. The impact assessments were conducted for the entire model rotations/orchards in order to explore cumulative effects as well as effects that depend on the farming systems (organic, integrated, and conventional). In arable cropping systems, herbicide tolerance had the most significant impact on agronomic practices in integrated and conventional farming systems. HT crops enable altered soil and weed management strategies. While no-till soil management benefited soil conservation, the highly efficient weed control reduced biodiversity. These effects accumulated over time due to the high proportion of HT crops in the integrated and conventional model rotations. In organic production systems, the effects were less pronounced, mainly due to non-use of herbicides. Traits affecting resistance to pests and diseases had a minor impact on the overall performance of the systems, mainly due to the availability of alternative crop protection tools or traditionally bred varieties. The use of GM crops had only a minor effect on the overall profitability of the arable crop rotations. In apple production systems, scab and fire blight resistance had a positive impact on natural resources as well as on local ecology due to the reduced need for spray passages and pesticide use. In integrated apple production, disease resistance increased profitability slightly, whereas in the organic scenario, both scab and fire blight resistance increased the profitability of the systems substantially. In conclusion, the ecological and socio-economic impacts identified in this study were highly context sensitive and were associated mainly with altered production systems rather than with the GM crops per se.