Abstract We describe efforts to epitaxially integrate GaAs with Si, using thin, relaxed Ge layers. The Ge films are deposited by molecular beam epitaxy using a self-assembled, selective-area growth technique, where atomic Ge etches an SiO 2 mask layer and then grows from pores extending to the Si substrate. The resulting Ge film coalesces over the SiO 2 mask and is planarized, using H 2O 2-based chemical–mechanical polishing. We subsequently deposit a GaAs/AlAs heterostructure on the polished Ge on Si substrate by metal-organic vapor phase epitaxy. While the initial Ge films were completely relaxed and dislocation-free, they contain a high density of stacking faults that propagate through the GaAs/AlAs heterostructure. These stacking faults create phase domains that appear as non-radiative recombination centers in cathodoluminescence images. Further development of two-step Ge epitaxy with an anneal near the Ge melting point eliminates stacking faults in the Ge, but decomposes the SiO 2 mask allowing threading dislocations to form and propagate through the GaAs/AlAs heterostructure. We discuss our strategy to prevent the loss of the SiO 2 mask and thus reduce threading dislocations.