In recent years the development of agro-food biotechnology - in particular the commercialisation of genetically engineered products - significantly differed between the EU and the USA. While in the first region of the global economy a quasi-moratorium was agreed on in 1999 preventing the commercial cultivation of transgenic crops in the EU, such plants are produced on millions of hectares in the USA and other parts of the world. This paper aims to give some insight in the effects of this differing situation on innovation activities in the field of agro-food biotechnology in the two regions. Therefore, the paper will firstly give a brief overview on regulatory principles and implementation activities in the field of agro-food biotechnology in the EU in comparison to the US system. Based on this background the development of specific indicators for innovation activities in this field will be compared for the EU and the USA. This relates e.g. to the character of research projects in the laboratory phase, scientific publications in this field, the deliberate release of genetically modified plants, the approval of such plants and the cultivation of transgenic crop in commercial agriculture. In addition, the relevance of additional factors for innovation activities in agro-food biotechnology in the EU is analysed in this paper thereby taking into account the view of differing actor groups, as well as the current debate on traceability and co-existence schemes between genetically modified crops, conventional agriculture and organic farming in the EU. Finally some conclusive general remarks will be drawn concerning the impacts of differing regulatory systems on innovation activities taking into account the experiences in other fields related to food production and food processing (e.g. Functional Food, organic farming and food processing).