The purpose of this study was to assess and describe the current spectrum of emerging zoonoses between 2000 and 2006 in European countries. A computerized search of the Medline database from January 1966 to August 2006 for all zoonotic agents in European countries was performed using specific criteria for emergence. Fifteen pathogens were identified as emerging in Europe from 2000 to August 2006: Rickettsiae spp., Anaplasma phagocytophilum, Borrelia burgdorferi, Bartonella spp., Francisella tularensis, Crimean Congo Haemorrhagic Fever Virus, Hantavirus, Toscana virus, Tick-borne encephalitis virus group, West Nile virus, Sindbis virus, Highly Pathogenic Avian influenza, variant Creutzfeldt–Jakob disease, Trichinella spp., and Echinococus multilocularis. Main risk factors included climatic variations, certain human activities as well as movements of animals, people or goods. Multi-disciplinary preventive strategies addressing these pathogens are of public health importance. Uniform harmonized case definitions should be introduced throughout Europe as true prevalence and incidence estimates are otherwise impossible.