Habitat transformation is the primary anthropogenic threat to global biodiversity. Fragmentation of reptile populations following habitat transformation within a landscape can lead to the extirpation of species. We investigated the effects of land-use on the species richness and abundance of reptile assemblages in three habitat types (two natural and one modified) in the grasslands of Gauteng, South Africa. Using trap arrays, we surveyed reptiles in primary grassland with little or no rock cover, primary grassland with large quartzite outcrops and scattered rocks, and secondary grasslands that were historically ploughed and cropped. We measured vegetation height and vegetation cover at these same localities. We caught significantly fewer reptile species in the historically cultivated sites than in either of the two natural habitat types. Differences in the reptile assemblage of each habitat type were not explained by either the spatial location or the vegetation structure of our trap sites but were well explained by the sites' habitat type. Estimates of total species richness indicated that we were able to adequately sample the reptile assemblages in the three habitat types, further supporting our observation of reduced species richness in the secondary grasslands. We infer that habitat transformation associated with cultivation e.g., rock removal, has had a detectable, negative impact on the species richness and composition of the local reptile assemblages. We recommend that land-use planning in Gauteng emphasise the need for areas of inter-connected, untransformed habitat in order to mitigate the negative impacts of habitat transformation on the local reptile diversity.