Transmission electron microscopy is a powerful imaging tool that has found broad application in materials science, nanoscience and biology1, 2, 3. With the introduction of aberration-corrected electron lenses, both the spatial resolution and the image quality in transmission electron microscopy have been significantly improved4, 5 and resolution below 0.5 ångströms has been demonstrated6. To reveal the three-dimensional (3D) structure of thin samples, electron tomography is the method of choice7, 8, 9, 10, 11, with cubic-nanometre resolution currently achievable10, 11. Discrete tomography has recently been used to generate a 3D atomic reconstruction of a silver nanoparticle two to three nanometres in diameter12, but this statistical method assumes prior knowledge of the particle’s lattice structure and requires that the atoms fit rigidly on that lattice. Here we report the experimental demonstration of a general electron tomography method that achieves atomic-scale resolution without initial assumptions about the sample structure. By combining a novel projection alignment and tomographic reconstruction method with scanning transmission electron microscopy, we have determined the 3D structure of an approximately ten-nanometre gold nanoparticle at 2.4-ångström resolution. Although we cannot definitively locate all of the atoms inside the nanoparticle, individual atoms are observed in some regions of the particle and several grains are identified in three dimensions. The 3D surface morphology and internal lattice structure revealed are consistent with a distorted icosahedral multiply twinned particle. We anticipate that this general method can be applied not only to determine the 3D structure of nanomaterials at atomic-scale resolution13, 14, 15, but also to improve the spatial resolution and image quality in other tomography fields7, 9, 16, 17, 18, 19, 20.