Indirect methods such as faecal counts have been widely used for assessing the abundance and habitat preferences of many mammal species, although their reliability has been long debated. We tested the validity of this method for the Eurasian badger Meles meles in a low-density population in northern Italy by comparing results obtained from radio-tracking and latrine distribution. The pattern of habitat use extrapolated from each method was strikingly similar, with badgers selecting for patches of woodland and avoiding agricultural and urban areas. Latrines were mainly sited in the centre of activity of all individuals along man-made linear features. Although our data need to be validated over a wider range of social groups, evidence suggests that latrines might be used to broadly infer habitat preferences of badgers at the landscape level in low-density areas.