Determining the three-dimensional (3D) arrangement of atoms in crystalline nanoparticles is important for nanometre-scale device engineering and also for applications involving nanoparticles, such as optoelectronics or catalysis. A nanoparticle’s physical and chemical properties are controlled by its exact 3D morphology, structure and composition1. Electron tomography enables the recovery of the shape of a nanoparticle from a series of projection images2, 3, 4. Although atomic-resolution electron microscopy has been feasible for nearly four decades, neither electron tomography nor any other experimental technique has yet demonstrated atomic resolution in three dimensions. Here we report the 3D reconstruction of a complex crystalline nanoparticle at atomic resolution. To achieve this, we combined aberration-corrected scanning transmission electron microscopy5, 6, 7, statistical parameter estimation theory8, 9 and discrete tomography10, 11. Unlike conventional electron tomography, only two images of the target—a silver nanoparticle embedded in an aluminium matrix—are sufficient for the reconstruction when combined with available knowledge about the particle’s crystallographic structure. Additional projections confirm the reliability of the result. The results we present help close the gap between the atomic resolution achievable in two-dimensional electron micrographs and the coarser resolution that has hitherto been obtained by conventional electron tomography.