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Background The rodentia and lagomorpha animals are the intermediate hosts of Echinococcus multilocularis, their distribution and infection of this parasite may facilitate the infection of definitive hosts such as dogs. The aim of this study was to determine the distribution of the intermediate hosts of Echinococcus multilocularis in Shiqu County, Sichuan, China.Methods A systematic sampling method was used to investigate the density of burrows of rodents and lagomorphs at 97 pasture sites in winter and summer pastureland and remote sensing (RS) technology was used to correlate their densities to the distribution of these animals in different landscape types.Results Based on the densities of Ochotona curzoniae, Microtus fuscus (dependent variable) and their burrow densities (independent variable) in survey points, regression equations were fitted respectively (Ochotona curzoniae, P＜0.0001, R2=0.8705; Microtus fuscus, P ＜0.0001, R2=0.9736). Their burrow density in summer pastureland was higher than in winter pastureland (F=36.65, P ＜0.0001). The burrow densities of Ochotona curzoniae and Microtus fuscus in bareland and half-bareland are higher than in grassland (F=7.73, P ＜0.001).Conclusions The regression relationship between the densities of Ochotona curzoniae and Microtus fuscus and their burrow densities indicate that the burrow densities could reflect the animal densities and that the burrow density was greater in summer pastureland than in winter pastureland. The main distribution areas of the intermediate hosts were in bareland and half-bareland.