In this work we demonstrate that a free-standing van der Waals heterostructure, usually regarded as a flat object, can exhibit an intrinsic buckled atomic structure resulting from the interaction between two layers with a small lattice mismatch. We studied a freely suspended membrane of well aligned graphene on a hexagonal boron nitride (hBN) monolayer by transmission electron microscopy (TEM) and scanning TEM (STEM). We developed a detection method in the STEM that is capable of recording the direction of the scattered electron beam and that is extremely sensitive to the local stacking of atoms. Comparison between experimental data and simulated models shows that the heterostructure effectively bends in the out-of-plane direction, producing an undulated structure having a periodicity that matches the moire wavelength. We attribute this rippling to the interlayer interaction and also show how this affects the intralayer strain in each layer.