In this paper, a two-stage growth method is reported for fabricating small and high-density Ge quantum dots on a Si(1 0 0) substrate. In the first stage coherent Ge islands with relatively large dimension but high density were grown based on the Stranski-Krastanov mode. A Si spacer layer was then deposited on the top of the Ge dots. In the second stage, smaller Ge dots were grown in the areas where the larger Ge islands exist under the Si spacer. The effective lateral scale of these dots is found to be less than 30 nm, and their vertical scale is less than 2 nm, as measured by atomic force microscopy and cross-sectional transmission electron microscopy.