The raccoon dog (Nyctereutes procyonoides) is an alien species in Europe and an important vector of zoonotic diseases. However, compared to the red fox (Vulpes vulpes), less attention has been paid to the raccoon dog as a potentially important host for Echinococcus multilocularis, the infective agent of alveolar echinococcosis, which is an emerging infectious disease with a high mortality rate. We examined the small intestines of 249 Estonian raccoon dogs and found 1.6% of individuals to be infected with E. multilocularis. The relatively large difference between this prevalence and that found in sympatric red foxes (31.5%) sampled during the same time period might be due to differences in diet: red foxes consume significantly more arvicolid rodents - the main intermediate hosts of the parasite - especially during the coldest period of the year when raccoon dogs hibernate. Nonetheless, given the relatively high density of raccoon dogs, our results suggest that the species also represents an important definitive host species for E. multilocularis in Estonia. Compared with other countries in Europe where E. multilocularis-infected raccoon dogs have been recorded (Latvia, Lithuania, Poland, Germany, and Slovakia), the prevalence in Estonia is low. The longer hibernation period of raccoon dogs at higher latitudes may explain this pattern. Both mitochondrial and nuclear loci were analysed for Estonian isolates: based on EmsB microsatellite genotyping the Estonian isolates shared an identical genotype with E. multilocularis in northern Poland, suggesting a common history with this region. The data from more than a quarter of the mitochondrial genome (3558 bp) revealed two novel haplotypes specific to Estonia and placed them into the same haplogroup with isolates from other European regions. Considering that the raccoon dog is becoming increasingly widespread and is already relatively abundant in several countries in Europe, the role of the species must be taken into account when assessing the E. multilocularis related risks to public health.