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Using an ultrahigh vacuum (UHV) scanning transmission electron microscope equipped with a molecular beam epitaxy chamber, the formation of the GaAs/Ge interface produced by deposition of GaAs on Ge substrate thin films with (111) or (110) or (100) orientations has been investigated. Three‐dimensional nucleation and growth of facetted GaAs epitaxial islands are characteristic of this interface. The formation energy and orientation of antiphase boundaries are obtained from the structure analysis of these ultrathin films.