The evolution of the shape and size distributions of Ge islands on Si(001) during annealing after deposition has been studied at different temperatures and effective coverages. The initial distributions of square-based pyramids, elongated “hut” structures, faceted “dome-shaped” islands, and much larger “superdomes” depends on the deposition conditions. During annealing after deposition, the islands coarsen over a limited range of times and temperatures. Those pyramidal-shaped islands that grow transform to faceted, dome-shaped islands as they become larger. Initially dome-shaped islands that dissolve transform to a pyramidal shape as they become smaller during the process of dissolving. Outside of this coarsening regime, the islands can achieve a relatively stable, steady-state configuration, especially at lower temperatures. At higher temperatures, intermixing of Si into the Ge islands dominates, decreasing the strain energy and allowing larger islands to form. At lower and intermediate temperatures, the initial wetting layer is metastable, and some Ge transfers to the islands during the early stages of annealing.