Conflicts between the conservation of biodiversity and other human activities have been and continue to be of increasing concern in the European Union, often having important political, economic, and environmental repercussions. These conflicts have been addressed in the European Union by using a wide array of top down and bottom up tools, with varying degrees of success. A new challenge is now facing Europe with the integration of 10 new countries in the European Union (EU) and an additional range of biodiversity-rich habitats placed under EU legislation. The rich biodiversity of the central and eastern European countries (CEEC) is likely to be threatened by some aspects of the integration process, and conflicts between the conservation of biodiversity and other human activities are expected. In this paper, we review certain existing conflicts between biodiversity conservation and human activities in the CEEC, expected conflicts associated with integration to the EU, particularly in terms of new policy and legislation implementation, and, finally, explore possible conflict management options.