Biotechnology offers extensive possibilities to incorporate new traits into organisms. Genetically modified (GM) traits relevant for agro-ecosystems include traits such as pest resistance and herbicide tolerance in crop plants, increased growth rate in fish and livestock, and enhanced nitrogen-fixation capabilities of soil microbes. In this review, we evaluated the direct and indirect trait-specific effects of GM plants, microbes, and animals on ecosystem processes and found that most of the effects of genetically modified organisms (GMOs) on ecosystem processes are indirect and are the result of associated changes in management strategy rather than a direct effect of the GMOs. Conflicting results on the performance and effects of GMOs are frequently reported, especially regarding crop yield and impacts on soil organisms. This is partly because methods with different levels of resolution have been used in different ecological contexts. Overall, there is little evidence that the effects of GM traits on ecosystem processes act with different mechanisms from those of traits modified using conventional methods. However, little is known about trait-specific effects of GMOs on ecosystem processes even though GMOs have been used for more than three decades. In particular, studies linking genetically modified traits to ecosystem processes at longer time scales are rare, but needed for evaluating trait effects, especially in an evolutionary context. In addition, biotechnology may provide a unique tool for gaining insights into the links between traits and ecosystem processes when integrated into basic ecological research. (C) 2015 Elsevier B.V. All rights reserved.