The Xinjiang Uygur autonomous region (XUAR) in north-western China is known to be endemic for Echinococcosis multilocularis, the causative agent of human alveolar echinococcosis (HAE). Despite regular reports of HAE cases in their region, very little is known about the local epidemiology of the disease or the transmission of E. multilocularis. The epidemiology of HAE in Xinjiang has now been investigated by the analysis of data collected from the medical records of 157 clinical cases who had attended the four main hospitals in the region. These data indicate that the disease is relatively common in the Altai, western Junggar, and Tianshan mountain ranges, whereas the Tarim and Junggar basins are likely to be of low endemicity. The prevalence of the disease in the Kunlun mountains is not clear. Semi-nomadic groups, especially those of Kazakh or Mongol origin, have a higher risk of infection than other ethnic groups. Prevalence of the disease in humans appears to be correlated with aspects of the local climate, such as annual precipitation and temperature. Red foxes, Microtinae, Ochotona spp. and Marmota spp. may be important hosts of E. multilocularis in the XUAR, sustaining the transmission cycles of the parasite.