The formation of Australia’s stony deserts 2–4 million years ago will have reduced the availability of suitable habitat for lizards extant at that time, particularly for fossorial species. For such taxa, mats of litter, which form underneath woody vegetation, may offer the only suitable refuge sites in a greater matrix of unsuitable stony and compacted clay habitat. The integrity of litter mats in Australia’s stony deserts is potentially threatened by trampling by large introduced herbivores and by surface flows during flood events. Here we assess the importance of litter mats as habitat for lizards in these stony deserts and determine the suitability of the mats in relation to disturbance regimes. We surveyed 85 sites in the stony desert in the extreme south of the Northern Territory, using hand-raking as the sampling technique. We located 85 individuals of eight lizard species from three families, including 18 individuals of the nationally vulnerable monotypic pygopodid Ophidiocephalus taeniatus, establishing the significance of this limited microhabitat. Lizards were located underneath mats produced from the litterfall of four species of Acacia shrubs, though were not evenly distributed across these four mat types. Our results also provide the first evidence of the impact of large introduced herbivores on the suitability of litter mats. Although this was not statistically significant, lizards were more likely to be located at sites without disturbance from large herbivores, and were located only under individual mats that exhibited no sign of disturbance.