Wild boar Sus scrofa L. rooting is a large and frequent disturbance, very extended all over the world. However, its impact in some sensitive habitats, such as alpine and subalpine grasslands remains unknown. These grasslands are considered important sites for biological conservation and traditional grazing activities, and are frequently affected by wild boar rootings. In this study, we selected three study sites representing a range of scenarios in Pyrenean alpine and subalpine grasslands, with differing protection status and grazing management. We assessed the extent of wild boar rooting, and determined the main variables that influence their distribution, taking into account the interactions among them. Our results showed that wild boar rooting significantly affected alpine and subalpine grasslands in the Pyrenees especially in protected non-hunting areas (up to 12% of the surface). The distribution of disturbed areas was influenced by a hierarchical suite of variables, among which vegetation, that is certain plant communities, was the most important. The apparent preference for dense grasslands might be associated with its soil depth, soil hardness and diversity of feeding resources. The importance of other variables, such as topography, distance to primary resources or grazing management, was site dependent. A broad understanding of the effects of variables and their relationships provide insights into the actual factors affecting the rooting selection. We hypothesize that the selection of feeding habitat, followed by the conditions of the soil to be uprooted and human management, are the main underlying factors that shape the distribution of wild boar rooting in alpine and subalpine grasslands.