An unambiguous determination of the three-dimensional structure of nanoparticles is challenging1. Electron tomography requires a series of images taken for many different specimen orientations2. This approach is ideal for stable and stationary structures3. But ultrasmall nanoparticles are intrinsically structurally unstable and may interact with the incident electron beam4, 5, 6, constraining the electron beam density that can be used and the duration of the observation. Here we use aberration-corrected scanning transmission electron microscopy7, coupled with simple imaging simulation, to determine with atomic resolution the size, three-dimensional shape, orientation and atomic arrangement of size-selected gold nanoclusters that are preformed in the gas phase and soft-landed on an amorphous carbon substrate. The structures of gold nanoclusters containing 3096 atoms can be identified with either Ino-decahedral, cuboctahedral or icosahedral geometries. Comparison with theoretical modelling of the system suggests that the structures are consistent with energetic considerations. The discovery that nanoscale gold particles function as active and selective catalysts for a variety of important chemical reactions has provoked much research interest in recent years8, 9, 10, 11, 12. We believe that the detailed structure information we provide will help to unravel the role of these nanoclusters in size- and structure-specific catalytic reactions11, 12. We note that the technique will be of use in investigations of other supported ultrasmall metal cluster systems.