Ex situ electron-beam lithography followed by conventional wet or dry etching has been used to pattern small holes of 60–150 nm wide, 10–40 nm deep in GaAs substrates. These holes then act as preferential nucleation sites for InAs dot growth. Preferential nucleation occurs due to a reduction in the apparent critical thickness above the pattern site, which is dependent on the dimensions of the initial pattern. We demonstrate that subsequent growth of site-controlled dots over the patterned sites varies with InAs deposition amount and growth temperature in a similar way to InAs dot growth on planar substrates. By varying temperature and either InAs deposition amount or pattern size, both the size and position of InAs quantum dots can be controlled.