We present a structural analysis of the graphene/Ru(0001) system obtained by surface x-ray diffraction. The data were fitted using Fourier-series-expanded displacement fields from an ideal bulk structure plus the application of symmetry constraints. The shape of the observed superstructure rods proves a reconstruction of the substrate, induced by strong bonding of graphene to ruthenium. Both the graphene layer and the underlying substrate are corrugated, with peak-to-peak heights of (0.82±0.15) Å and (0.19±0.02) Å for graphene and the topmost Ru-atomic layer, respectively. The Ru corrugation decays slowly over several monolayers into the bulk. The system also exhibits chirality, whereby in-plane rotations of up to 2.0° in those regions of the superstructure where the graphene is weakly bound are driven by elastic energy minimization.