The self-assembly of different nanocrystals into a binary superlattice is of interest for both colloidal science and nanomaterials science. New properties may emerge from the interaction between the nanocrystal building blocks that are ordered in close contact in three dimensions. Identification of the superlattice structure including its defects is of key interest in understanding the electrical and optical properties of these systems. Transmission electron microscopy (TEM) has been very instrumental to reach this goal but fails for complex crystal structures and buried defects. Here, we use electron tomography to resolve the three-dimensional crystal structure of a binary superlattice that could not be resolved by TEM only. The structure with a [PbSe] 6[CdSe]19 stoichiometry has no analogue in the atomic world. Moreover we will show how tomography can overcome the clouding effects of planar defects on structure identification by TEM.