It is widely believed that carrier-density inhomogeneities (“electron-hole puddles”) in single-layer graphene on a substrate such as quartz are due to charged impurities located close to the graphene sheet. Here we demonstrate by using a Kohn-Sham-Dirac density-functional scheme that corrugations in a real sample are sufficient to determine electron-hole puddles on length scales that are larger than the spatial resolution of state-of-the-art scanning tunneling microscopy.