Doping is a process in which atomic impurities are intentionally added to a host material to modify its properties. It has had a revolutionary impact in altering or introducing electronic, magnetic, luminescent, and catalytic properties for several applications, for example in semiconductors. Here we explore and demonstrate the extension of the concept of substitutional atomic doping to nanometre-scale crystal doping, in which one nanocrystal is used to replace another to form doped self-assembled superlattices. Towards this goal, we show that gold nanocrystals act as substitutional dopants in superlattices of cadmium selenide or lead selenide nanocrystals when the size of the gold nanocrystal is very close to that of the host. The gold nanocrystals occupy random positions in the superlattice and their density is readily and widely controllable, analogous to the case of atomic doping, but here through nanocrystal self-assembly. We also show that the electronic properties of the superlattices are highly tunable and strongly affected by the presence and density of the gold nanocrystal dopants. The conductivity of lead selenide films, for example, can be manipulated over at least six orders of magnitude by the addition of gold nanocrystals and is explained by a percolation model. As this process relies on the self-assembly of uniform nanocrystals, it can be generally applied to assemble a wide variety of nanocrystal-doped structures for electronic, optical, magnetic, and catalytic materials.