Ge islands fabricated on Si(100) by molecular beam epitaxy at different growth temperatures, were studied using crosssectional scanning transmission electron microscopy and energy-dispersive X-ray spectrometry combined with electron energy loss spectrometry experiments. The island size, shape, strain, and material composition define the dot-related optical transition energies, but they are all strongly dependent on the growth temperature. We have performed quantitative investigations of the material composition of Ge/Si(001) quantum dots. The samples were grown at temperatures ranging from 430 to 730 °C, with one buried and one uncapped layer of Ge islands separated by 140 nm intrinsic Si. The measurements showed a Ge concentration very close to 100 % in the islands of samples grown at 430 °C. With a growth temperature of 530 °C, a ~20 % reduction of the Ge fraction was observed, which is due to intermixing of Si and Ge. This is consistent with our previous photoluminescence results, which revealed a significant blue shift of the Ge dot-related emission peak in this growth temperature range. The Ge concentration decreases more slowly when the growth temperature is increased above 600 °C, which can be explained by geometrical arguments. The longer distance between the interface and the core of these larger sized dome-shaped islands implies that less Si atoms reach the dot center. In general, the uncapped Ge dots have similar widths as the embedded islands, but the height is almost exclusively larger. Furthermore, the Ge concentration is slightly lower for the overgrown dots.