SUMMARY Human alveolar echinococcosis, caused by the tapeworm Echinococcus multilocularis, is the most pathogenic parasitozoonosis in the temperate and arctic region of Europe. E. multilocularis adult worms were detected in foxes of 16 Hungarian counties and in the suburban areas of the capital, Budapest. The prevalence of infection was 10.7% and 7.9%, the intensity of infection was 746 and 243 worms/fox in 2008–2009 and 2012–2013, respectively. The spatial distribution of the parasite was highly clumped; the majority of infected foxes came from the Northern Mountain Range and northern part of Transdanubia. The multi-locus microsatellite analysis of the worms indicate that Hungary should be considered as a peripheral area of a single European focus, where the dispersal movement of foxes resulted in the spreading of the parasite from one county to another within a time period short enough to avoid a substantial genetic drift. Based on geographic information system-based analysis, mean annual temperature and annual precipitation were the major determinants of the spatial distribution of E. multilocularis in Hungary. It can be attributed to the sensitivity of E. multilocularis eggs to high temperatures and desiccation. Although spreading and emergence of the parasite was observed in Hungary before 2009, the prevalence and intensity of infection did not change significantly between the two collection periods. It can be explained by the considerably lower annual precipitation before the second collection period.