The long-tailed ground squirrels Spermophilus undulatus represent the most abundant burrowing herbivorous species in the southern Altai grasslands and are suggested to play an important role in the maintenance of this mountain ecosystem. The aim of this study was to identify the key features that influence their habitat use in the southern part of the Altai Republic (south-west Siberia, Russia). The research area represents a complete sequence of altitudinal vegetation zones from steppe, forest-steppe, forest, sub-alpine and alpine tundra. Our results suggest that S. undulatus prefers short-grass steppes, near the water source and with a thin layer of a chernozem soil containing a large amount of coarse clastics. The species strictly avoids forests and tolerates only a low density of bush cover. Altitude and exposure to sun do not represent significant factors in the habitat choice of S. undulatus. Neither the presence of pikas nor the presence of marmots influences habitat selection of the ground squirrels. Strong preferences for habitats near a water source may limit the distribution of the species to mountain areas. Degree of human disturbance was not a significant factor affecting distribution and the species even displays slight preferences for heavily grazed habitat near human settlements and roads. Intensive grazing prevents shrubs and forest invasion, keeps vegetation low and thus provides appropriate conditions for the ground squirrels, favouring an open habitat where predators can be easily detected by sight. Our results suggest that the habitat selection of ground squirrels may be determined rather by a protection from predators and burrowing conditions than by food availability.