Rabies remains endemic within a number of countries in Southeast Europe including Romania, Bulgaria and Turkey. With the probable expansion of the European Union eastwards, it is likely that rabies elimination programs will be increased to reduce the burden of disease in new accession countries. A clear understanding of the epidemiology of the virus in this area of Europe is vital before such programs are introduced. With the exception of Turkey, the red fox (Vulpes vulpes) is the principal disease reservoir in Southeastern Europe. However, cases of rabies in the dog (Canis familiaris) are regularly reported. In contrast to Northern Europe, the raccoon dog (Nyctereutes procyonoides) does not appear to be a vector in the south. This study summarises the current rabies situation in Southeast Europe and demonstrates the phylogenetic relationships between the viruses in a number of the countries within the region. Rabies virus RNA was extracted from original samples and a fragment of the nucleoprotein gene amplified by reverse-transcriptase PCR. Automated sequencing was used to derive nucleoprotein gene sequences and these were used to prepare a molecular phylogeny of rabies viruses in Southeast Europe. In Bulgaria, the dog is the main vector bringing rabies into contact with humans and livestock. However, other species may also act as reservoirs for the disease, complicating the development of elimination strategies. The fox is the principal reservoir species for rabies in Romania although cases in dogs are regularly reported. Despite a gradual decline in dog rabies, urban pockets of the disease remain in many regions of Turkey. Furthermore, there is some evidence that the fox has been a significant vectorfor rabies and may be responsible for increases in rabies in cattle in the Aegean region of the country. Throughout the region there is evidence for cross-border movement of rabies by both wildlife and canine vectors.