The benefits of using ontologies have been recognised in many areas such as knowledge and content management, electronic commerce and recently the emerging field of the Semantic Web. These new applications can be seen as a great success of research in ontologies. On the other hand, moving into real application comes with new challenges that need to be addressed on a principled level rather than for specific applications. This special issue will be devoted to less well-explored topics that have come into focus recently as a response to the new problems we face when trying to use ontologies in heterogeneous distributed environments. These environments include the use of ontologies in peer-to-peer and pervasive computing systems.