Rabies, a worldwide zoonosis, remains a public-health concern despite oral wildlife vaccination in Europe. After a ten-year break, Macedonia reported eight rabies cases in 2011-2012. Two countries (Serbia and Bulgaria) bordering Macedonia are reporting cases in domestic and wild animals. This report describes the genetic characterisation of eight isolates from Macedonia compared with representative samples from neighbouring countries. All of the isolates tested belong to the Eastern European group, with a high degree of nucleotide sequence identity in the nucleoprotein gene. The close genetic relationship between isolates from the three bordering countries suggests that wildlife is responsible for rabies movements in the region.