Agricultural activities and road construction have been reported as major causes of landscape fragmentation. We have assessed the distribution of warrens of a burrowing mammal, the European rabbit (Oryctolagus cuniculus), in natural vegetation patches within an agricultural mosaic crossed by a highway. The rabbit is considered a key species in Mediterranean ecosystems because of both, its role as a prey, and as an engineering species. We have specifically considered the occurrence and abundance of warrens (a group of entrances < 2 m from each other) as well as their size (number of entrances) and their spatial distribution within natural vegetation patches. Results showed that rabbit occurrence is more likely in natural vegetation patches with steeper slopes, more circular shapes and closer to the highway. In addition, there were more warrens in larger patches and larger warrens were found in larger, steeper, elongated patches. More frequent presence and greater warren abundance found close to the highway may be due to the barrier effect, but attraction due to habitat suitability and protection from predators have also been suggested in the literature. Besides the relevance of the different mechanisms implied, our results suggest that the presence of roads modifies the presence of rabbit warrens across a fragmented agricultural landscape. In this sense, roads could impact rabbit density and, therefore, present relevant implications for the population persistence of this species; also, roads could indirectly affect the distribution and welfare of rabbits' predators.