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GaN/AlN heterostructures grown by molecular beam epitaxy are studied by high-resolution transmission electron microscopy (HRTEM). The two-dimensional/three-dimensional Stranski–Krastanow growth mode transition of GaN allows the formation of GaN quantum-dot structures embedded in AlN. The nature of the wetting layer associated with these dots is determined by quantitative HRTEM analysis, based on comparison between interplanar distortion profiles of experimental and simulated images. This study demonstrates a low intermixing between GaN and AlN materials. Such result is also evidenced for the GaN dots.