Use of biotechnology in agricultural and food production has become one the most controversial issue in the last decade. Food safety is a crucial aspect of human life and therefore it is an issue of prime importance to the EU, however research on transition countries is practically nonexistent. We focus on Hungary, Slovakia, the Czech Republic, Slovenia and Romania using a Key Technology Survey, to analyse the biotechnologies that might have a strong impact upon food quality and health. We first investigate the likely future impacts of biotechnology on food safety than we employ foresight methodology. Third we apply cross-country comparison instead focusing on just one country. Results suggest that CEE countries are laggards in the development and application of biotechnology. We find that experts evaluate rather positively the effects of biotechnology on various types of hazards and large differences can be observed among country experts to assess these impacts.