Using high resolution electron microscopy and extensive image simulation, the atomic structure of the inversion boundaries has been determined in GaN layers grown on sapphire by electron cyclotron resonance assisted molecular beam epitaxy. They form nanometric domains (5–20 nm) limited by {101¯0} planes crossing the whole epitaxial layer. These small dimensions excluded the use of more conventional microscopy methods such as convergent beam diffraction for their characterization. For image simulations, up to 10 models including the well known Austerman–Gehman and Holt ones were considered for the boundary atomic structure. The overall agreement with the observed contrast was reached for a Holt type model of structure in which the boundary plane contains two wrong bonds per atom. Although the overall atomic configuration is neutral in {101¯0} boundary planes, it is expected to be highly energetic in ionic materials like GaN due to the difference in Ga–Ga and N–N bond length and local charge difference. This may probably explain the small size of the domains observed in the present samples. ©1997 American Institute of Physics.